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Retapamulin and Capreomycin bound to the 50S subunit

Electron Microscopy
1.83Å resolution
PDB entry 8ceu coloured by chain, front view.
PDB entry 8ceu coloured by chain, side view.
PDB entry 8ceu coloured by chain, top view.
Source organisms:
Assembly composition:
hetero 38-mer (preferred)
Entry contents: 29 distinct polypeptide molecules
2 distinct RNA molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero 38-mer
Accessible surface area: 427811.63 Å2
Buried surface area: 221047.97 Å2
Dissociation area: 203.64 Å2
Dissociation energy (ΔGdiss): -3.24 kcal/mol
Dissociation entropy (TΔSdiss): 5.97 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-272138

Macromolecules

Large ribosomal subunit protein bL33
Chain: 0
Length: 55 amino acids
Theoretical weight: 6.39 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7N9 (Residues: 1-55; Coverage: 100%)
Gene names: JW3611, b3636, rpmG
Pfam: Ribosomal protein L33
Large ribosomal subunit protein bL33 in PDB entry 8ceu, assembly 1, front view.
Large ribosomal subunit protein bL33 in PDB entry 8ceu, assembly 1, side view.
Large ribosomal subunit protein bL33 in PDB entry 8ceu, assembly 1, top view.
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Large ribosomal subunit protein bL34
Chain: 1
Length: 46 amino acids
Theoretical weight: 5.4 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7P5 (Residues: 1-46; Coverage: 100%)
Gene names: JW3680, b3703, rimA, rpmH, ssaF
Pfam: Ribosomal protein L34
Large ribosomal subunit protein bL34 in PDB entry 8ceu, assembly 1, front view.
Large ribosomal subunit protein bL34 in PDB entry 8ceu, assembly 1, side view.
Large ribosomal subunit protein bL34 in PDB entry 8ceu, assembly 1, top view.
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Large ribosomal subunit protein bL35
Chain: 2
Length: 65 amino acids
Theoretical weight: 7.31 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7Q1 (Residues: 1-65; Coverage: 100%)
Gene names: JW1707, b1717, rpmI
Pfam: Ribosomal protein L35
Large ribosomal subunit protein bL35 in PDB entry 8ceu, assembly 1, front view.
Large ribosomal subunit protein bL35 in PDB entry 8ceu, assembly 1, side view.
Large ribosomal subunit protein bL35 in PDB entry 8ceu, assembly 1, top view.
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Large ribosomal subunit protein bL36A
Chain: 3
Length: 38 amino acids
Theoretical weight: 4.38 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7Q6 (Residues: 1-38; Coverage: 100%)
Gene names: JW3261, b3299, rpmJ
Pfam: Ribosomal protein L36
Large ribosomal subunit protein bL36A in PDB entry 8ceu, assembly 1, front view.
Large ribosomal subunit protein bL36A in PDB entry 8ceu, assembly 1, side view.
Large ribosomal subunit protein bL36A in PDB entry 8ceu, assembly 1, top view.
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Large ribosomal subunit protein uL2
Chain: c
Length: 273 amino acids
Theoretical weight: 29.92 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P60422 (Residues: 1-273; Coverage: 100%)
Gene names: JW3279, b3317, rplB
Pfam:
Large ribosomal subunit protein uL2 in PDB entry 8ceu, assembly 1, front view.
Large ribosomal subunit protein uL2 in PDB entry 8ceu, assembly 1, side view.
Large ribosomal subunit protein uL2 in PDB entry 8ceu, assembly 1, top view.
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Large ribosomal subunit protein uL3
Chain: d
Length: 209 amino acids
Theoretical weight: 22.29 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P60438 (Residues: 1-209; Coverage: 100%)
Gene names: JW3282, b3320, rplC
Pfam: Ribosomal protein L3
Large ribosomal subunit protein uL3 in PDB entry 8ceu, assembly 1, front view.
Large ribosomal subunit protein uL3 in PDB entry 8ceu, assembly 1, side view.
Large ribosomal subunit protein uL3 in PDB entry 8ceu, 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 BW25113
UniProt:
  • Canonical: P60723 (Residues: 1-201; Coverage: 100%)
Gene names: JW3281, b3319, eryA, rplD
Pfam: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL4 in PDB entry 8ceu, assembly 1, front view.
Large ribosomal subunit protein uL4 in PDB entry 8ceu, assembly 1, side view.
Large ribosomal subunit protein uL4 in PDB entry 8ceu, 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 BW25113
UniProt:
  • Canonical: P62399 (Residues: 1-179; Coverage: 100%)
Gene names: JW3270, b3308, rplE
Pfam:
Large ribosomal subunit protein uL5 in PDB entry 8ceu, assembly 1, front view.
Large ribosomal subunit protein uL5 in PDB entry 8ceu, assembly 1, side view.
Large ribosomal subunit protein uL5 in PDB entry 8ceu, 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 BW25113
UniProt:
  • Canonical: P0AG55 (Residues: 1-177; Coverage: 100%)
Gene names: JW3267, b3305, rplF
Pfam: Ribosomal protein L6
Large ribosomal subunit protein uL6 in PDB entry 8ceu, assembly 1, front view.
Large ribosomal subunit protein uL6 in PDB entry 8ceu, assembly 1, side view.
Large ribosomal subunit protein uL6 in PDB entry 8ceu, 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 BW25113
UniProt:
  • Canonical: P0A7R1 (Residues: 1-149; Coverage: 100%)
Gene names: JW4161, b4203, rplI
Pfam:
Large ribosomal subunit protein bL9 in PDB entry 8ceu, assembly 1, front view.
Large ribosomal subunit protein bL9 in PDB entry 8ceu, assembly 1, side view.
Large ribosomal subunit protein bL9 in PDB entry 8ceu, assembly 1, top view.
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Large ribosomal subunit protein uL13
Chain: i
Length: 142 amino acids
Theoretical weight: 16.05 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0AA10 (Residues: 1-142; Coverage: 100%)
Gene names: JW3200, b3231, rplM
Pfam: Ribosomal protein L13
Large ribosomal subunit protein uL13 in PDB entry 8ceu, assembly 1, front view.
Large ribosomal subunit protein uL13 in PDB entry 8ceu, assembly 1, side view.
Large ribosomal subunit protein uL13 in PDB entry 8ceu, assembly 1, top view.
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Large ribosomal subunit protein uL14
Chain: j
Length: 123 amino acids
Theoretical weight: 13.57 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0ADY3 (Residues: 1-123; Coverage: 100%)
Gene names: JW3272, b3310, rplN
Pfam: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL14 in PDB entry 8ceu, assembly 1, front view.
Large ribosomal subunit protein uL14 in PDB entry 8ceu, assembly 1, side view.
Large ribosomal subunit protein uL14 in PDB entry 8ceu, assembly 1, top view.
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Large ribosomal subunit protein uL15
Chain: k
Length: 144 amino acids
Theoretical weight: 15.01 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P02413 (Residues: 1-144; Coverage: 100%)
Gene names: JW3263, b3301, rplO
Pfam: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL15 in PDB entry 8ceu, assembly 1, front view.
Large ribosomal subunit protein uL15 in PDB entry 8ceu, assembly 1, side view.
Large ribosomal subunit protein uL15 in PDB entry 8ceu, assembly 1, top view.
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Large ribosomal subunit protein uL16
Chain: l
Length: 136 amino acids
Theoretical weight: 15.33 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0ADY7 (Residues: 1-136; Coverage: 100%)
Gene names: JW3275, b3313, rplP
Pfam: Ribosomal protein L16p/L10e
Large ribosomal subunit protein uL16 in PDB entry 8ceu, assembly 1, front view.
Large ribosomal subunit protein uL16 in PDB entry 8ceu, assembly 1, side view.
Large ribosomal subunit protein uL16 in PDB entry 8ceu, assembly 1, top view.
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Large ribosomal subunit protein bL17
Chain: m
Length: 127 amino acids
Theoretical weight: 14.39 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0AG44 (Residues: 1-127; Coverage: 100%)
Gene names: JW3256, b3294, rplQ
Pfam: Ribosomal protein L17
Large ribosomal subunit protein bL17 in PDB entry 8ceu, assembly 1, front view.
Large ribosomal subunit protein bL17 in PDB entry 8ceu, assembly 1, side view.
Large ribosomal subunit protein bL17 in PDB entry 8ceu, assembly 1, top view.
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Large ribosomal subunit protein uL18
Chain: n
Length: 117 amino acids
Theoretical weight: 12.79 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0C018 (Residues: 1-117; Coverage: 100%)
Gene names: JW3266, b3304, rplR
Pfam: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Large ribosomal subunit protein uL18 in PDB entry 8ceu, assembly 1, front view.
Large ribosomal subunit protein uL18 in PDB entry 8ceu, assembly 1, side view.
Large ribosomal subunit protein uL18 in PDB entry 8ceu, assembly 1, top view.
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Large ribosomal subunit protein bL19
Chain: o
Length: 115 amino acids
Theoretical weight: 13.16 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7K6 (Residues: 1-115; Coverage: 100%)
Gene names: JW2587, b2606, rplS
Pfam: Ribosomal protein L19
Large ribosomal subunit protein bL19 in PDB entry 8ceu, assembly 1, front view.
Large ribosomal subunit protein bL19 in PDB entry 8ceu, assembly 1, side view.
Large ribosomal subunit protein bL19 in PDB entry 8ceu, assembly 1, top view.
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Large ribosomal subunit protein bL20
Chain: p
Length: 118 amino acids
Theoretical weight: 13.53 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7L3 (Residues: 1-118; Coverage: 100%)
Gene names: JW1706, b1716, pdzA, rplT
Pfam: Ribosomal protein L20
Large ribosomal subunit protein bL20 in PDB entry 8ceu, assembly 1, front view.
Large ribosomal subunit protein bL20 in PDB entry 8ceu, assembly 1, side view.
Large ribosomal subunit protein bL20 in PDB entry 8ceu, assembly 1, top view.
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Large ribosomal subunit protein bL21
Chain: q
Length: 103 amino acids
Theoretical weight: 11.59 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0AG48 (Residues: 1-103; Coverage: 100%)
Gene names: JW3153, b3186, rplU
Pfam: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein bL21 in PDB entry 8ceu, assembly 1, front view.
Large ribosomal subunit protein bL21 in PDB entry 8ceu, assembly 1, side view.
Large ribosomal subunit protein bL21 in PDB entry 8ceu, assembly 1, top view.
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Large ribosomal subunit protein uL22
Chain: r
Length: 110 amino acids
Theoretical weight: 12.25 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P61175 (Residues: 1-110; Coverage: 100%)
Gene names: JW3277, b3315, eryB, rplV
Pfam: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL22 in PDB entry 8ceu, assembly 1, front view.
Large ribosomal subunit protein uL22 in PDB entry 8ceu, assembly 1, side view.
Large ribosomal subunit protein uL22 in PDB entry 8ceu, assembly 1, top view.
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Large ribosomal subunit protein uL23
Chain: s
Length: 100 amino acids
Theoretical weight: 11.22 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0ADZ0 (Residues: 1-100; Coverage: 100%)
Gene names: JW3280, b3318, rplW
Pfam: Ribosomal protein L23
Large ribosomal subunit protein uL23 in PDB entry 8ceu, assembly 1, front view.
Large ribosomal subunit protein uL23 in PDB entry 8ceu, assembly 1, side view.
Large ribosomal subunit protein uL23 in PDB entry 8ceu, assembly 1, top view.
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Large ribosomal subunit protein uL24
Chain: t
Length: 104 amino acids
Theoretical weight: 11.34 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P60624 (Residues: 1-104; Coverage: 100%)
Gene names: JW3271, b3309, rplX
Pfam:
Large ribosomal subunit protein uL24 in PDB entry 8ceu, assembly 1, front view.
Large ribosomal subunit protein uL24 in PDB entry 8ceu, assembly 1, side view.
Large ribosomal subunit protein uL24 in PDB entry 8ceu, assembly 1, top view.
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Large ribosomal subunit protein bL25
Chain: u
Length: 94 amino acids
Theoretical weight: 10.71 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P68919 (Residues: 1-94; Coverage: 100%)
Gene names: JW2173, b2185, rplY
Pfam: Ribosomal L25p family
Large ribosomal subunit protein bL25 in PDB entry 8ceu, assembly 1, front view.
Large ribosomal subunit protein bL25 in PDB entry 8ceu, assembly 1, side view.
Large ribosomal subunit protein bL25 in PDB entry 8ceu, assembly 1, top view.
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Large ribosomal subunit protein bL27
Chain: v
Length: 85 amino acids
Theoretical weight: 9.15 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7L8 (Residues: 1-85; Coverage: 100%)
Gene names: JW3152, b3185, rpmA
Pfam: Ribosomal L27 protein
Large ribosomal subunit protein bL27 in PDB entry 8ceu, assembly 1, front view.
Large ribosomal subunit protein bL27 in PDB entry 8ceu, assembly 1, side view.
Large ribosomal subunit protein bL27 in PDB entry 8ceu, assembly 1, top view.
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Large ribosomal subunit protein bL28
Chain: w
Length: 78 amino acids
Theoretical weight: 9.03 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7M2 (Residues: 1-78; Coverage: 100%)
Gene names: JW3612, b3637, rpmB
Pfam: Ribosomal L28 family
Large ribosomal subunit protein bL28 in PDB entry 8ceu, assembly 1, front view.
Large ribosomal subunit protein bL28 in PDB entry 8ceu, assembly 1, side view.
Large ribosomal subunit protein bL28 in PDB entry 8ceu, assembly 1, top view.
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Large ribosomal subunit protein uL29
Chain: x
Length: 63 amino acids
Theoretical weight: 7.29 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7M6 (Residues: 1-63; Coverage: 100%)
Gene names: JW3274, b3312, rpmC
Pfam: Ribosomal L29 protein
Large ribosomal subunit protein uL29 in PDB entry 8ceu, assembly 1, front view.
Large ribosomal subunit protein uL29 in PDB entry 8ceu, assembly 1, side view.
Large ribosomal subunit protein uL29 in PDB entry 8ceu, assembly 1, top view.
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Large ribosomal subunit protein uL30
Chain: y
Length: 59 amino acids
Theoretical weight: 6.55 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0AG51 (Residues: 1-59; Coverage: 100%)
Gene names: JW3264, b3302, rpmD
Pfam: Ribosomal protein L30p/L7e
Large ribosomal subunit protein uL30 in PDB entry 8ceu, assembly 1, front view.
Large ribosomal subunit protein uL30 in PDB entry 8ceu, assembly 1, side view.
Large ribosomal subunit protein uL30 in PDB entry 8ceu, assembly 1, top view.
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Large ribosomal subunit protein bL32
Chain: z
Length: 57 amino acids
Theoretical weight: 6.46 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7N4 (Residues: 1-57; Coverage: 100%)
Gene names: JW1075, b1089, rpmF
Pfam: Ribosomal L32p protein family
Large ribosomal subunit protein bL32 in PDB entry 8ceu, assembly 1, front view.
Large ribosomal subunit protein bL32 in PDB entry 8ceu, assembly 1, side view.
Large ribosomal subunit protein bL32 in PDB entry 8ceu, assembly 1, top view.
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Capreomycin IA
Chains: C, D, E, F, G, H, I, V
Length: 6 amino acids
Theoretical weight: 687 Da
Source organism: Streptomyces californicus
Expression system: Not provided
Capreomycin IA in PDB entry 8ceu, assembly 1, front view.
Capreomycin IA in PDB entry 8ceu, assembly 1, side view.
Capreomycin IA in PDB entry 8ceu, assembly 1, top view.
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RNA chain a
Name: 23S ribosomal RNA
Representative chains: a
Length: 2904 nucleotides
Theoretical weight: 941.81 KDa
Rfam: Bacterial large subunit ribosomal RNA
23S ribosomal RNA in PDB entry 8ceu, assembly 1, front view.
23S ribosomal RNA in PDB entry 8ceu, assembly 1, side view.
23S ribosomal RNA in PDB entry 8ceu, 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 8ceu, assembly 1, front view.
5S ribosomal RNA in PDB entry 8ceu, assembly 1, side view.
5S ribosomal RNA in PDB entry 8ceu, assembly 1, top view.
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