SMTL ID : 8cgi.1

Pentacycline TP038 bound to the 30S head

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 1.89 Å

Oligo State

hetero-1-1-1-1-1-1-1-1-mer

Ligands

1 x P8F: Pentacycline(Non-functional Binders)

P8F.1: 9 residues within 4Å: Chain B: G.966, G.1053, C.1054, C.1195, A.1196, A.1197, G.1198 Ligands: MG.20, MG.34 No protein-ligand interaction detected (PLIP)

10 x K: POTASSIUM ION(Non-functional Binders)(Non-covalent)

K.2: 4 residues within 4Å: Chain B: G.976, C.1359, G.1361, A.1362 No protein-ligand interaction detected (PLIP) K.3: 5 residues within 4Å: Chain B: A.949, G.971, G.1233, C.1234, U.1364 No protein-ligand interaction detected (PLIP) K.4: 5 residues within 4Å: Chain B: U.1073, G.1074, A.1082, U.1083, G.1084 No protein-ligand interaction detected (PLIP) K.5: 3 residues within 4Å: Chain B: A.1319, C.1322, G.1323 No protein-ligand interaction detected (PLIP) K.6: 3 residues within 4Å: Chain B: C.1303, G.1304, G.1305 No protein-ligand interaction detected (PLIP) K.37: 4 residues within 4Å: Chain B: U.943, G.944, G.945, G.1337 No protein-ligand interaction detected (PLIP) K.38: 5 residues within 4Å: Chain B: U.1224, A.1225, C.1322 Chain G: G.99, Q.100 No protein-ligand interaction detected (PLIP) K.39: 5 residues within 4Å: Chain B: A.978, C.979, G.1222, C.1322 Ligands: MG.23 No protein-ligand interaction detected (PLIP) K.40: 5 residues within 4Å: Chain B: G.1053, G.1058, C.1059, G.1198, U.1199 No protein-ligand interaction detected (PLIP) K.41: 5 residues within 4Å: Chain B: G.1241, G.1242, C.1243, G.1294, U.1295 No protein-ligand interaction detected (PLIP)

32 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.7: 2 residues within 4Å: Chain B: G.944, G.945 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Chain B: U.1224 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain B: C.979, C.980 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain B: C.1109, A.1110, U.1189 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain B: U.1095, G.1108 No protein-ligand interaction detected (PLIP) MG.12: 4 residues within 4Å: Chain B: A.1067, G.1068, G.1094, G.1387 No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Chain B: C.1069 No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Chain B: C.934 No protein-ligand interaction detected (PLIP) MG.15: 1 residues within 4Å: Chain B: A.937 No protein-ligand interaction detected (PLIP) MG.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.17: 1 residues within 4Å: Chain H: Q.60 No protein-ligand interaction detected (PLIP) MG.18: 1 residues within 4Å: Chain B: G.1048 No protein-ligand interaction detected (PLIP) MG.19: 4 residues within 4Å: Chain B: G.963, A.964, G.1198, U.1199 No protein-ligand interaction detected (PLIP) MG.20: 5 residues within 4Å: Chain B: C.1054, A.1196, A.1197, G.1198 Ligands: P8F.1 No protein-ligand interaction detected (PLIP) MG.21: 4 residues within 4Å: Chain B: G.1053, C.1054, A.1196, A.1197 No protein-ligand interaction detected (PLIP) MG.22: 1 residues within 4Å: Chain B: C.962 No protein-ligand interaction detected (PLIP) MG.23: 7 residues within 4Å: Chain B: C.979, C.980, U.981, U.982, G.1222, C.1223 Ligands: K.39 No protein-ligand interaction detected (PLIP) MG.24: 1 residues within 4Å: Chain B: G.1370 No protein-ligand interaction detected (PLIP) MG.25: 1 residues within 4Å: Chain B: C.972 No protein-ligand interaction detected (PLIP) MG.26: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.27: 2 residues within 4Å: Chain B: C.1303, G.1304 No protein-ligand interaction detected (PLIP) MG.28: 3 residues within 4Å: Chain B: C.1284, A.1285, G.1355 No protein-ligand interaction detected (PLIP) MG.29: 3 residues within 4Å: Chain B: G.1050, C.1051, C.1208 No protein-ligand interaction detected (PLIP) MG.30: 2 residues within 4Å: Chain B: A.1329, G.1331 No protein-ligand interaction detected (PLIP) MG.31: 2 residues within 4Å: Chain B: A.1238, U.1335 No protein-ligand interaction detected (PLIP) MG.32: 1 residues within 4Å: Chain B: G.1013 No protein-ligand interaction detected (PLIP) MG.33: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.34: 2 residues within 4Å: Chain B: G.966 Ligands: P8F.1 No protein-ligand interaction detected (PLIP) MG.35: 2 residues within 4Å: Chain B: G.1300, G.1334 No protein-ligand interaction detected (PLIP) MG.36: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.42: 6 residues within 4Å: Chain B: C.1051, U.1052, C.1200, U.1205, G.1206, G.1207 No protein-ligand interaction detected (PLIP) MG.43: 4 residues within 4Å: Chain B: U.1330 Chain G: T.20, I.22, V.25 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:T.20, G:I.22, G:V.25, H2O.15, H2O.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Paternoga, H. et al., Structural conservation of antibiotic interaction with ribosomes. Nat.Struct.Mol.Biol. (2023)

Release Date

2023-07-26

Peptides

Large ribosomal subunit protein bL31A: A
Small ribosomal subunit protein uS3: C
30S ribosomal protein S7: D
Small ribosomal subunit protein uS9: E
Small ribosomal subunit protein uS10: F
Small ribosomal subunit protein uS13: G
Small ribosomal subunit protein uS14: H
Small ribosomal subunit protein uS19: I

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
4

C
C

D
G

E
I

F
J

G
M

H
N

I
S

Large ribosomal subunit protein bL31A

Small ribosomal subunit protein uS3

30S ribosomal protein S7

Small ribosomal subunit protein uS9

Small ribosomal subunit protein uS10

Small ribosomal subunit protein uS13

Small ribosomal subunit protein uS14

Small ribosomal subunit protein uS19

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