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Structure of a bacterial 50S ribosomal subunit in complex with the novel quinoxolidinone antibiotic cadazolid

Electron Microscopy
3Å resolution
PDB entry 6qul coloured by chain, front view.
PDB entry 6qul coloured by chain, side view.
PDB entry 6qul coloured by chain, top view.
Source organism: Escherichia coli
Assembly composition:
hetero 31-mer (preferred)
Entry contents: 28 distinct polypeptide molecules
3 distinct RNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Large ribosomal protein and RNA
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Multimeric state: hetero 31-mer
Accessible surface area: 456091.36 Å2
Buried surface area: 192685.18 Å2
Dissociation area: 600.54 Å2
Dissociation energy (ΔGdiss): -0.08 kcal/mol
Dissociation entropy (TΔSdiss): 10.66 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-249958

Macromolecules

Large ribosomal subunit protein uL2
Chain: C
Length: 273 amino acids
Theoretical weight: 29.92 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P60422 (Residues: 1-273; Coverage: 100%)
Gene names: JW3279, b3317, rplB
Pfam:
InterPro:
CATH:
Large ribosomal subunit protein uL2 in PDB entry 6qul, assembly 1, front view.
Large ribosomal subunit protein uL2 in PDB entry 6qul, assembly 1, side view.
Large ribosomal subunit protein uL2 in PDB entry 6qul, assembly 1, top view.
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Large ribosomal subunit protein uL3
Chain: D
Length: 209 amino acids
Theoretical weight: 22.28 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P60438 (Residues: 1-209; Coverage: 100%)
Gene names: JW3282, b3320, rplC
Pfam: Ribosomal protein L3
InterPro:
Large ribosomal subunit protein uL3 in PDB entry 6qul, assembly 1, front view.
Large ribosomal subunit protein uL3 in PDB entry 6qul, assembly 1, side view.
Large ribosomal subunit protein uL3 in PDB entry 6qul, assembly 1, top view.
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Large ribosomal subunit protein uL4
Chain: E
Length: 201 amino acids
Theoretical weight: 22.12 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P60723 (Residues: 1-201; Coverage: 100%)
Gene names: JW3281, b3319, eryA, rplD
Pfam: Ribosomal protein L4/L1 family
InterPro:
Large ribosomal subunit protein uL4 in PDB entry 6qul, assembly 1, front view.
Large ribosomal subunit protein uL4 in PDB entry 6qul, assembly 1, side view.
Large ribosomal subunit protein uL4 in PDB entry 6qul, assembly 1, top view.
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Large ribosomal subunit protein uL5
Chain: F
Length: 179 amino acids
Theoretical weight: 20.33 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P62399 (Residues: 1-179; Coverage: 100%)
Gene names: JW3270, b3308, rplE
Pfam:
InterPro:
Large ribosomal subunit protein uL5 in PDB entry 6qul, assembly 1, front view.
Large ribosomal subunit protein uL5 in PDB entry 6qul, assembly 1, side view.
Large ribosomal subunit protein uL5 in PDB entry 6qul, assembly 1, top view.
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Large ribosomal subunit protein uL6
Chain: G
Length: 177 amino acids
Theoretical weight: 18.93 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0AG55 (Residues: 1-177; Coverage: 100%)
Gene names: JW3267, b3305, rplF
Pfam: Ribosomal protein L6
InterPro:
Large ribosomal subunit protein uL6 in PDB entry 6qul, assembly 1, front view.
Large ribosomal subunit protein uL6 in PDB entry 6qul, assembly 1, side view.
Large ribosomal subunit protein uL6 in PDB entry 6qul, assembly 1, top view.
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Large ribosomal subunit protein bL9
Chain: H
Length: 149 amino acids
Theoretical weight: 15.79 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7R1 (Residues: 1-149; Coverage: 100%)
Gene names: JW4161, b4203, rplI
Pfam:
InterPro:
Large ribosomal subunit protein bL9 in PDB entry 6qul, assembly 1, front view.
Large ribosomal subunit protein bL9 in PDB entry 6qul, assembly 1, side view.
Large ribosomal subunit protein bL9 in PDB entry 6qul, assembly 1, top view.
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Large ribosomal subunit protein uL13
Chain: K
Length: 142 amino acids
Theoretical weight: 16.05 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0AA10 (Residues: 1-142; Coverage: 100%)
Gene names: JW3200, b3231, rplM
Pfam: Ribosomal protein L13
InterPro:
Large ribosomal subunit protein uL13 in PDB entry 6qul, assembly 1, front view.
Large ribosomal subunit protein uL13 in PDB entry 6qul, assembly 1, side view.
Large ribosomal subunit protein uL13 in PDB entry 6qul, assembly 1, top view.
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Large ribosomal subunit protein uL14
Chain: L
Length: 123 amino acids
Theoretical weight: 13.57 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0ADY3 (Residues: 1-123; Coverage: 100%)
Gene names: JW3272, b3310, rplN
Pfam: Ribosomal protein L14p/L23e
InterPro:
CATH: Ribosomal protein L14
Large ribosomal subunit protein uL14 in PDB entry 6qul, assembly 1, front view.
Large ribosomal subunit protein uL14 in PDB entry 6qul, assembly 1, side view.
Large ribosomal subunit protein uL14 in PDB entry 6qul, assembly 1, top view.
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Large ribosomal subunit protein uL15
Chain: M
Length: 144 amino acids
Theoretical weight: 15.01 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P02413 (Residues: 1-144; Coverage: 100%)
Gene names: JW3263, b3301, rplO
Pfam: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
InterPro:
Large ribosomal subunit protein uL15 in PDB entry 6qul, assembly 1, front view.
Large ribosomal subunit protein uL15 in PDB entry 6qul, assembly 1, side view.
Large ribosomal subunit protein uL15 in PDB entry 6qul, assembly 1, top view.
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Large ribosomal subunit protein uL16
Chain: N
Length: 136 amino acids
Theoretical weight: 15.31 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0ADY7 (Residues: 1-136; Coverage: 100%)
Gene names: JW3275, b3313, rplP
Pfam: Ribosomal protein L16p/L10e
InterPro:
CATH: Ribosomal protein L10e/L16
Large ribosomal subunit protein uL16 in PDB entry 6qul, assembly 1, front view.
Large ribosomal subunit protein uL16 in PDB entry 6qul, assembly 1, side view.
Large ribosomal subunit protein uL16 in PDB entry 6qul, assembly 1, top view.
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Large ribosomal subunit protein bL17
Chain: O
Length: 127 amino acids
Theoretical weight: 14.39 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0AG44 (Residues: 1-127; Coverage: 100%)
Gene names: JW3256, b3294, rplQ
Pfam: Ribosomal protein L17
InterPro:
CATH: Ribosomal protein L17
Large ribosomal subunit protein bL17 in PDB entry 6qul, assembly 1, front view.
Large ribosomal subunit protein bL17 in PDB entry 6qul, assembly 1, side view.
Large ribosomal subunit protein bL17 in PDB entry 6qul, assembly 1, top view.
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Large ribosomal subunit protein uL18
Chain: P
Length: 117 amino acids
Theoretical weight: 12.79 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0C018 (Residues: 1-117; Coverage: 100%)
Gene names: JW3266, b3304, rplR
Pfam: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
InterPro:
CATH: Nucleotidyltransferase; domain 5
Large ribosomal subunit protein uL18 in PDB entry 6qul, assembly 1, front view.
Large ribosomal subunit protein uL18 in PDB entry 6qul, assembly 1, side view.
Large ribosomal subunit protein uL18 in PDB entry 6qul, assembly 1, top view.
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Large ribosomal subunit protein bL19
Chain: Q
Length: 115 amino acids
Theoretical weight: 13.16 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7K6 (Residues: 1-115; Coverage: 100%)
Gene names: JW2587, b2606, rplS
Pfam: Ribosomal protein L19
InterPro:
Large ribosomal subunit protein bL19 in PDB entry 6qul, assembly 1, front view.
Large ribosomal subunit protein bL19 in PDB entry 6qul, assembly 1, side view.
Large ribosomal subunit protein bL19 in PDB entry 6qul, assembly 1, top view.
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Large ribosomal subunit protein bL20
Chain: R
Length: 118 amino acids
Theoretical weight: 13.53 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7L3 (Residues: 1-118; Coverage: 100%)
Gene names: JW1706, b1716, pdzA, rplT
Pfam: Ribosomal protein L20
InterPro:
Large ribosomal subunit protein bL20 in PDB entry 6qul, assembly 1, front view.
Large ribosomal subunit protein bL20 in PDB entry 6qul, assembly 1, side view.
Large ribosomal subunit protein bL20 in PDB entry 6qul, assembly 1, top view.
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Large ribosomal subunit protein bL21
Chain: S
Length: 103 amino acids
Theoretical weight: 11.59 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0AG48 (Residues: 1-103; Coverage: 100%)
Gene names: JW3153, b3186, rplU
Pfam: Ribosomal prokaryotic L21 protein
InterPro:
Large ribosomal subunit protein bL21 in PDB entry 6qul, assembly 1, front view.
Large ribosomal subunit protein bL21 in PDB entry 6qul, assembly 1, side view.
Large ribosomal subunit protein bL21 in PDB entry 6qul, assembly 1, top view.
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Large ribosomal subunit protein uL22
Chain: T
Length: 110 amino acids
Theoretical weight: 12.25 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P61175 (Residues: 1-110; Coverage: 100%)
Gene names: JW3277, b3315, eryB, rplV
Pfam: Ribosomal protein L22p/L17e
InterPro:
CATH: Ribosomal protein L22/L17
Large ribosomal subunit protein uL22 in PDB entry 6qul, assembly 1, front view.
Large ribosomal subunit protein uL22 in PDB entry 6qul, assembly 1, side view.
Large ribosomal subunit protein uL22 in PDB entry 6qul, assembly 1, top view.
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Large ribosomal subunit protein uL23
Chain: U
Length: 100 amino acids
Theoretical weight: 11.22 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0ADZ0 (Residues: 1-100; Coverage: 100%)
Gene names: JW3280, b3318, rplW
Pfam: Ribosomal protein L23
InterPro:
CATH: Alpha-Beta Plaits
Large ribosomal subunit protein uL23 in PDB entry 6qul, assembly 1, front view.
Large ribosomal subunit protein uL23 in PDB entry 6qul, assembly 1, side view.
Large ribosomal subunit protein uL23 in PDB entry 6qul, assembly 1, top view.
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Large ribosomal subunit protein uL24
Chain: V
Length: 104 amino acids
Theoretical weight: 11.34 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P60624 (Residues: 1-104; Coverage: 100%)
Gene names: JW3271, b3309, rplX
Pfam:
InterPro:
Large ribosomal subunit protein uL24 in PDB entry 6qul, assembly 1, front view.
Large ribosomal subunit protein uL24 in PDB entry 6qul, assembly 1, side view.
Large ribosomal subunit protein uL24 in PDB entry 6qul, assembly 1, top view.
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Large ribosomal subunit protein bL25
Chain: W
Length: 94 amino acids
Theoretical weight: 10.71 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P68919 (Residues: 1-94; Coverage: 100%)
Gene names: JW2173, b2185, rplY
Pfam: Ribosomal L25p family
InterPro:
CATH: Ribosomal Protein L25; Chain P
Large ribosomal subunit protein bL25 in PDB entry 6qul, assembly 1, front view.
Large ribosomal subunit protein bL25 in PDB entry 6qul, assembly 1, side view.
Large ribosomal subunit protein bL25 in PDB entry 6qul, assembly 1, top view.
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Large ribosomal subunit protein bL27
Chain: X
Length: 85 amino acids
Theoretical weight: 9.15 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7L8 (Residues: 1-85; Coverage: 100%)
Gene names: JW3152, b3185, rpmA
Pfam: Ribosomal L27 protein
InterPro:
Large ribosomal subunit protein bL27 in PDB entry 6qul, assembly 1, front view.
Large ribosomal subunit protein bL27 in PDB entry 6qul, assembly 1, side view.
Large ribosomal subunit protein bL27 in PDB entry 6qul, assembly 1, top view.
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Large ribosomal subunit protein bL28
Chain: Y
Length: 78 amino acids
Theoretical weight: 9.03 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7M2 (Residues: 1-78; Coverage: 100%)
Gene names: JW3612, b3637, rpmB
Pfam: Ribosomal L28 family
InterPro:
Large ribosomal subunit protein bL28 in PDB entry 6qul, assembly 1, front view.
Large ribosomal subunit protein bL28 in PDB entry 6qul, assembly 1, side view.
Large ribosomal subunit protein bL28 in PDB entry 6qul, assembly 1, top view.
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Large ribosomal subunit protein uL29
Chain: Z
Length: 63 amino acids
Theoretical weight: 7.29 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7M6 (Residues: 1-63; Coverage: 100%)
Gene names: JW3274, b3312, rpmC
Pfam: Ribosomal L29 protein
InterPro:
Large ribosomal subunit protein uL29 in PDB entry 6qul, assembly 1, front view.
Large ribosomal subunit protein uL29 in PDB entry 6qul, assembly 1, side view.
Large ribosomal subunit protein uL29 in PDB entry 6qul, assembly 1, top view.
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Large ribosomal subunit protein uL30
Chain: a
Length: 59 amino acids
Theoretical weight: 6.55 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0AG51 (Residues: 1-59; Coverage: 100%)
Gene names: JW3264, b3302, rpmD
Pfam: Ribosomal protein L30p/L7e
InterPro:
CATH: Ribosomal protein L30, ferredoxin-like fold domain
Large ribosomal subunit protein uL30 in PDB entry 6qul, assembly 1, front view.
Large ribosomal subunit protein uL30 in PDB entry 6qul, assembly 1, side view.
Large ribosomal subunit protein uL30 in PDB entry 6qul, assembly 1, top view.
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Large ribosomal subunit protein bL32
Chain: b
Length: 57 amino acids
Theoretical weight: 6.46 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7N4 (Residues: 1-57; Coverage: 100%)
Gene names: JW1075, b1089, rpmF
Pfam: Ribosomal L32p protein family
InterPro:
Large ribosomal subunit protein bL32 in PDB entry 6qul, assembly 1, front view.
Large ribosomal subunit protein bL32 in PDB entry 6qul, assembly 1, side view.
Large ribosomal subunit protein bL32 in PDB entry 6qul, assembly 1, top view.
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Large ribosomal subunit protein bL33
Chain: c
Length: 55 amino acids
Theoretical weight: 6.39 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7N9 (Residues: 1-55; Coverage: 100%)
Gene names: JW3611, b3636, rpmG
Pfam: Ribosomal protein L33
InterPro:
CATH: Ribosomal protein L33
Large ribosomal subunit protein bL33 in PDB entry 6qul, assembly 1, front view.
Large ribosomal subunit protein bL33 in PDB entry 6qul, assembly 1, side view.
Large ribosomal subunit protein bL33 in PDB entry 6qul, assembly 1, top view.
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Large ribosomal subunit protein bL34
Chain: d
Length: 46 amino acids
Theoretical weight: 5.4 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7P5 (Residues: 1-46; Coverage: 100%)
Gene names: JW3680, b3703, rimA, rpmH, ssaF
Pfam: Ribosomal protein L34
InterPro:
CATH: Helix Hairpins
Large ribosomal subunit protein bL34 in PDB entry 6qul, assembly 1, front view.
Large ribosomal subunit protein bL34 in PDB entry 6qul, assembly 1, side view.
Large ribosomal subunit protein bL34 in PDB entry 6qul, assembly 1, top view.
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Large ribosomal subunit protein bL35
Chain: e
Length: 65 amino acids
Theoretical weight: 7.31 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7Q1 (Residues: 1-65; Coverage: 100%)
Gene names: JW1707, b1717, rpmI
Pfam: Ribosomal protein L35
InterPro:
Large ribosomal subunit protein bL35 in PDB entry 6qul, assembly 1, front view.
Large ribosomal subunit protein bL35 in PDB entry 6qul, assembly 1, side view.
Large ribosomal subunit protein bL35 in PDB entry 6qul, assembly 1, top view.
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Large ribosomal subunit protein bL36A
Chain: f
Length: 38 amino acids
Theoretical weight: 4.38 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7Q6 (Residues: 1-38; Coverage: 100%)
Gene names: JW3261, b3299, rpmJ
Pfam: Ribosomal protein L36
InterPro:
Large ribosomal subunit protein bL36A in PDB entry 6qul, assembly 1, front view.
Large ribosomal subunit protein bL36A in PDB entry 6qul, assembly 1, side view.
Large ribosomal subunit protein bL36A in PDB entry 6qul, assembly 1, top view.
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RNA chain 1
Name: P-site fMet-tRNA(fMet)
Representative chains: 1
Length: 4 nucleotides
Theoretical weight: 1.22 KDa
P-site fMet-tRNA(fMet) in PDB entry 6qul, assembly 1, front view.
P-site fMet-tRNA(fMet) in PDB entry 6qul, assembly 1, side view.
P-site fMet-tRNA(fMet) in PDB entry 6qul, assembly 1, top view.
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RNA chain A
Name: 23S ribosomal RNA
Representative chains: A
Length: 2795 nucleotides
Theoretical weight: 906.51 KDa
Rfam: Bacterial large subunit ribosomal RNA
23S ribosomal RNA in PDB entry 6qul, assembly 1, front view.
23S ribosomal RNA in PDB entry 6qul, assembly 1, side view.
23S ribosomal RNA in PDB entry 6qul, assembly 1, top view.
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RNA chain B
Name: 5S ribosomal RNA
Representative chains: B
Length: 120 nucleotides
Theoretical weight: 38.79 KDa
Rfam: 5S ribosomal RNA
5S ribosomal RNA in PDB entry 6qul, assembly 1, front view.
5S ribosomal RNA in PDB entry 6qul, assembly 1, side view.
5S ribosomal RNA in PDB entry 6qul, assembly 1, top view.
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