› 6czr

X-ray diffraction
3.14Å resolution

The structure of amicetin bound to the 70S ribosome

Released:
DOI: 10.2210/pdb6czr/pdb
PDB entry 6czr coloured by chain, front view.
PDB entry 6czr coloured by chain, side view.
PDB entry 6czr coloured by chain, top view.
Source organism: Thermus thermophilus HB8
Primary publication:
Unifying the Aminohexopyranose- and Peptidyl-Nucleoside Antibiotics: Implications for Antibiotic Design
Serrano CM, Kanna Reddy HR, Eiler DR, Koch MR, Tresco BIC, Barrows LR, VanderLinden RT, Testa CA, Sebahar PR, Looper RE
Angew. Chem. Int. Ed. Engl. 132 11426-11429 (2020)

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 52-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-143763 (preferred)
Entry contents:
49 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (52 distinct):
Large ribosomal subunit protein uL2 Chains: 1D, 2D
Molecule details ›
Chains: 1D, 2D
Length: 275 amino acids
Theoretical weight: 30.4 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60405 (Residues: 2-276; Coverage: 100%)
Gene names: TTHA1689, rplB
Sequence domains:
Large ribosomal subunit protein uL3 Chains: 1E, 2E
Molecule details ›
Chains: 1E, 2E
Length: 204 amino acids
Theoretical weight: 22.25 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN8 (Residues: 1-204; Coverage: 99%)
Gene names: TTHA1692, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chains: 1F, 2F
Molecule details ›
Chains: 1F, 2F
Length: 203 amino acids
Theoretical weight: 22.51 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN9 (Residues: 6-208; Coverage: 97%)
Gene names: TTHA1691, rplD
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5 Chains: 1G, 2G
Molecule details ›
Chains: 1G, 2G
Length: 181 amino acids
Theoretical weight: 20.93 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ0 (Residues: 2-182; Coverage: 100%)
Gene names: TTHA1680, rplE
Sequence domains:
Large ribosomal subunit protein uL6 Chains: 1H, 2H
Molecule details ›
Chains: 1H, 2H
Length: 174 amino acids
Theoretical weight: 18.98 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P0DOY8 (Residues: 2-175; Coverage: 97%)
Gene names: TTHA1677, rplF
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein bL9 Chains: 1I, 2I
Molecule details ›
Chains: 1I, 2I
Length: 147 amino acids
Theoretical weight: 16.29 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLQ1 (Residues: 1-147; Coverage: 99%)
Gene names: TTHA0242, rplI
Sequence domains:
Large ribosomal subunit protein uL13 Chains: 1N, 2N
Molecule details ›
Chains: 1N, 2N
Length: 140 amino acids
Theoretical weight: 15.93 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60488 (Residues: 1-140; Coverage: 100%)
Gene names: TTHA1465, rplM
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14 Chains: 1O, 2O
Molecule details ›
Chains: 1O, 2O
Length: 122 amino acids
Theoretical weight: 13.32 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP8 (Residues: 1-122; Coverage: 100%)
Gene names: TTHA1682, rplN
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL15 Chains: 1P, 2P
Molecule details ›
Chains: 1P, 2P
Length: 149 amino acids
Theoretical weight: 16.25 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ7 (Residues: 1-149; Coverage: 99%)
Gene names: TTHA1673, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16 Chains: 1Q, 2Q
Molecule details ›
Chains: 1Q, 2Q
Length: 141 amino acids
Theoretical weight: 15.99 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60489 (Residues: 1-141; Coverage: 100%)
Gene names: TTHA1685, rplP
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein bL17 Chains: 1R, 2R
Molecule details ›
Chains: 1R, 2R
Length: 118 amino acids
Theoretical weight: 13.75 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q9Z9H5 (Residues: 1-118; Coverage: 100%)
Gene names: TTHA1663, rpl17, rplQ
Sequence domains: Ribosomal protein L17
Large ribosomal subunit protein uL18 Chains: 1S, 2S
Molecule details ›
Chains: 1S, 2S
Length: 110 amino acids
Theoretical weight: 12.44 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ4 (Residues: 3-112; Coverage: 98%)
Gene names: TTHA1676, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Large ribosomal subunit protein bL19 Chains: 1T, 2T
Molecule details ›
Chains: 1T, 2T
Length: 131 amino acids
Theoretical weight: 15.5 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60490 (Residues: 1-131; Coverage: 90%)
Gene names: TTHA1031, rplS
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20 Chains: 1U, 2U
Molecule details ›
Chains: 1U, 2U
Length: 116 amino acids
Theoretical weight: 13.59 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60491 (Residues: 2-117; Coverage: 98%)
Gene names: TTHA0553, rplT
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21 Chains: 1V, 2V
Molecule details ›
Chains: 1V, 2V
Length: 101 amino acids
Theoretical weight: 11.07 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60492 (Residues: 1-101; Coverage: 100%)
Gene names: TTHA1783, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22 Chains: 1W, 2W
Molecule details ›
Chains: 1W, 2W
Length: 112 amino acids
Theoretical weight: 12.68 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP3 (Residues: 1-112; Coverage: 99%)
Gene names: TTHA1687, rplV
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23 Chains: 1X, 2X
Molecule details ›
Chains: 1X, 2X
Length: 95 amino acids
Theoretical weight: 10.65 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP0 (Residues: 1-95; Coverage: 99%)
Gene names: TTHA1690, rplW
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24 Chains: 1Y, 2Y
Molecule details ›
Chains: 1Y, 2Y
Length: 107 amino acids
Theoretical weight: 11.73 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP9 (Residues: 1-107; Coverage: 97%)
Gene names: TTHA1681, rplX
Sequence domains:
Large ribosomal subunit protein bL25 Chains: 1Z, 2Z
Molecule details ›
Chains: 1Z, 2Z
Length: 203 amino acids
Theoretical weight: 22.85 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHZ1 (Residues: 1-203; Coverage: 99%)
Gene names: TTHA1589, rpl25, rplY, rptL5
Sequence domains:
Large ribosomal subunit protein bL27 Chains: 10, 20
Molecule details ›
Chains: 10, 20
Length: 77 amino acids
Theoretical weight: 8.69 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60493 (Residues: 8-84; Coverage: 91%)
Gene names: TTHA1782, rpmA
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL28 Chains: 11, 21
Molecule details ›
Chains: 11, 21
Length: 97 amino acids
Theoretical weight: 10.87 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60494 (Residues: 2-98; Coverage: 99%)
Gene names: TTHA0042, rpmB
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29 Chains: 12, 22
Molecule details ›
Chains: 12, 22
Length: 70 amino acids
Theoretical weight: 8.49 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP6 (Residues: 1-70; Coverage: 97%)
Gene names: TTHA1684, rpmC
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL30 Chains: 13, 23
Molecule details ›
Chains: 13, 23
Length: 59 amino acids
Theoretical weight: 6.67 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ6 (Residues: 2-60; Coverage: 98%)
Gene names: TTHA1674, rpmD
Sequence domains: Ribosomal protein L30p/L7e
Large ribosomal subunit protein bL31 Chains: 14, 24
Molecule details ›
Chains: 14, 24
Length: 69 amino acids
Theoretical weight: 8.09 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJE1 (Residues: 1-69; Coverage: 97%)
Gene names: TTHA1073, rpmE
Sequence domains: Ribosomal protein L31
Large ribosomal subunit protein bL32 Chains: 15, 25
Molecule details ›
Chains: 15, 25
Length: 59 amino acids
Theoretical weight: 6.59 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80339 (Residues: 2-60; Coverage: 98%)
Gene names: TTHA0418, rpl32, rpmF
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL33 Chains: 16, 26
Molecule details ›
Chains: 16, 26
Length: 53 amino acids
Theoretical weight: 6.5 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P35871 (Residues: 2-54; Coverage: 98%)
Gene names: TTHA0250, rpl33, rpmG
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein bL34 Chains: 17, 27
Molecule details ›
Chains: 17, 27
Length: 48 amino acids
Theoretical weight: 5.98 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80340 (Residues: 1-48; Coverage: 98%)
Gene names: TTHA0446, rpl34, rpmH
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein bL35 Chains: 18, 28
Molecule details ›
Chains: 18, 28
Length: 64 amino acids
Theoretical weight: 7.37 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SKU1 (Residues: 2-65; Coverage: 99%)
Gene names: TTHA0552, rpmI
Sequence domains: Ribosomal protein L35
Large ribosomal subunit protein bL36 Chains: 19, 29
Molecule details ›
Chains: 19, 29
Length: 37 amino acids
Theoretical weight: 4.44 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHR2 (Residues: 1-37; Coverage: 100%)
Gene names: TTHA1668, rpmJ
Sequence domains: Ribosomal protein L36
Small ribosomal subunit protein uS2 Chains: 1b, 2b
Molecule details ›
Chains: 1b, 2b
Length: 231 amino acids
Theoretical weight: 26.65 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80371 (Residues: 7-237; Coverage: 90%)
Gene names: TTHA0861, rps2, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chains: 1c, 2c
Molecule details ›
Chains: 1c, 2c
Length: 206 amino acids
Theoretical weight: 22.86 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80372 (Residues: 2-207; Coverage: 86%)
Gene names: TTHA1686, rps3, rpsC
Sequence domains:
Small ribosomal subunit protein uS4 Chains: 1d, 2d
Molecule details ›
Chains: 1d, 2d
Length: 208 amino acids
Theoretical weight: 24.24 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80373 (Residues: 2-209; Coverage: 100%)
Gene names: TTHA1665, rps4, rpsD
Sequence domains:
Small ribosomal subunit protein uS5 Chains: 1e, 2e
Molecule details ›
Chains: 1e, 2e
Length: 148 amino acids
Theoretical weight: 16.14 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ5 (Residues: 5-152; Coverage: 91%)
Gene names: TTHA1675, rpsE
Sequence domains:
Small ribosomal subunit protein bS6 Chains: 1f, 2f
Molecule details ›
Chains: 1f, 2f
Length: 100 amino acids
Theoretical weight: 11.92 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLP8 (Residues: 1-100; Coverage: 99%)
Gene names: TTHA0245, rpsF
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein uS7 Chains: 1g, 2g
Molecule details ›
Chains: 1g, 2g
Length: 155 amino acids
Theoretical weight: 17.92 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P17291 (Residues: 2-156; Coverage: 99%)
Gene names: TTHA1696, rps7, rpsG
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS8 Chains: 1h, 2h
Molecule details ›
Chains: 1h, 2h
Length: 137 amino acids
Theoretical weight: 15.74 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P0DOY9 (Residues: 2-138; Coverage: 99%)
Gene names: TTHA1678, rpsH
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS9 Chains: 1i, 2i
Molecule details ›
Chains: 1i, 2i
Length: 127 amino acids
Theoretical weight: 14.28 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80374 (Residues: 2-128; Coverage: 99%)
Gene names: TTHA1464, rps9, rpsI
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10 Chains: 1j, 2j
Molecule details ›
Chains: 1j, 2j
Length: 97 amino acids
Theoretical weight: 11.17 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN7 (Residues: 4-100; Coverage: 92%)
Gene names: TTHA1693, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS11 Chains: 1k, 2k
Molecule details ›
Chains: 1k, 2k
Length: 114 amino acids
Theoretical weight: 12.03 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80376 (Residues: 13-126; Coverage: 88%)
Gene names: TTHA1666, rps11, rpsK
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chains: 1l, 2l
Molecule details ›
Chains: 1l, 2l
Length: 122 amino acids
Theoretical weight: 13.65 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN3 (Residues: 2-123; Coverage: 92%)
Gene names: TTHA1697, rpsL
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS13 Chains: 1m, 2m
Molecule details ›
Chains: 1m, 2m
Length: 116 amino acids
Theoretical weight: 13.24 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80377 (Residues: 2-117; Coverage: 92%)
Gene names: TTHA1667, rps13, rpsM
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS14 Chains: 1n, 2n
Molecule details ›
Chains: 1n, 2n
Length: 60 amino acids
Theoretical weight: 7.03 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P0DOY6 (Residues: 2-61; Coverage: 98%)
Gene names: TTHA1679, rpsN, rpsZ
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS15 Chains: 1o, 2o
Molecule details ›
Chains: 1o, 2o
Length: 88 amino acids
Theoretical weight: 10.45 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJ76 (Residues: 2-89; Coverage: 99%)
Gene names: TTHA1138, rpsO
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16 Chains: 1p, 2p
Molecule details ›
Chains: 1p, 2p
Length: 82 amino acids
Theoretical weight: 9.8 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJH3 (Residues: 1-82; Coverage: 93%)
Gene names: TTHA1035, rpsP
Sequence domains: Ribosomal protein S16
Small ribosomal subunit protein uS17 Chains: 1q, 2q
Molecule details ›
Chains: 1q, 2q
Length: 99 amino acids
Theoretical weight: 11.72 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P0DOY7 (Residues: 2-100; Coverage: 94%)
Gene names: TTHA1683, rpsQ
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein bS18 Chains: 1r, 2r
Molecule details ›
Chains: 1r, 2r
Length: 68 amino acids
Theoretical weight: 7.9 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLQ0 (Residues: 20-87; Coverage: 77%)
Gene names: TTHA0243, rpsR
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein uS19 Chains: 1s, 2s
Molecule details ›
Chains: 1s, 2s
Length: 83 amino acids
Theoretical weight: 9.46 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP2 (Residues: 2-84; Coverage: 89%)
Gene names: TTHA1688, rpsS
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein bS20 Chains: 1t, 2t
Molecule details ›
Chains: 1t, 2t
Length: 98 amino acids
Theoretical weight: 10.88 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80380 (Residues: 6-103; Coverage: 93%)
Gene names: TTHA1397, rps20, rpsT
Sequence domains: Ribosomal protein S20
Small ribosomal subunit protein bTHX Chains: 1u, 2u
Molecule details ›
Chains: 1u, 2u
Length: 23 amino acids
Theoretical weight: 2.83 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SIH3 (Residues: 2-24; Coverage: 85%)
Gene names: TTHA1396, rpsU
Sequence domains: 30S ribosomal protein Thx
23S ribosomal RNA Chains: 1A, 2A
Molecule details ›
Chains: 1A, 2A
Length: 2915 nucleotides
Theoretical weight: 948.05 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chains: 1B, 2B
Molecule details ›
Chains: 1B, 2B
Length: 120 nucleotides
Theoretical weight: 38.88 KDa
Sequence domains: 5S ribosomal RNA
16S ribosomal RNA Chains: 1a, 2a
Molecule details ›
Chains: 1a, 2a
Length: 2331 nucleotides
Theoretical weight: 755.32 KDa
Sequence domains: Bacterial small subunit ribosomal RNA

Ligands and Environments

6 bound ligands:
Ligand MG 1933 x MG
Ligand ARG 2 x ARG
Ligand MPD 7 x MPD
Ligand FSD 2 x FSD
Ligand ZN 9 x ZN
Ligand SF4 2 x SF4
14 modified residues:
Ligand PSU 8 x PSU
Ligand 5MU 4 x 5MU
Ligand OMC 2 x OMC
Ligand 5MC 12 x 5MC
Ligand OMG 2 x OMG
Ligand 2MA 2 x 2MA
Ligand OMU 2 x OMU
Ligand G7M 2 x G7M
Ligand M2G 2 x M2G
Ligand 2MG 2 x 2MG
Ligand 4OC 2 x 4OC
Ligand UR3 2 x UR3
Ligand MA6 4 x MA6
Ligand 0TD 2 x 0TD

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P212121
Unit cell:
a: 210.04Å b: 449.52Å c: 624.08Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.241 0.238 0.292

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