SMTL ID : 9h9k.1

Complex 3 (HEAD) 30S-tRNA-GE81112

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x A- A- U- G- U: mRNA (5'-R(P*AP*AP*UP*GP*U)-3')(Non-functional Binders)

A-A-U-G-U.1: 4 residues within 4Å: Chain B: C.35, A.36, U.37, A.38 Protein-ligand interaction information (PLIP) not available

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

MG.2: 2 residues within 4Å: Chain A: A.1110, U.1189 No protein-ligand interaction detected (PLIP) MG.3: 4 residues within 4Å: Chain A: C.1352, G.1353, C.1369, G.1370 No protein-ligand interaction detected (PLIP) MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain A: A.1176, G.1177, G.1178 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain A: G.963, A.964, U.1199 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain A: C.972 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain A: C.1223, U.1224 No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain A: G.1053, C.1054, A.1196, A.1197 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain A: G.1300, A.1333, G.1334 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain A: A.937, A.938 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain A: A.1357 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Chain A: C.1303, G.1304 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain A: A.1329, G.1331 No protein-ligand interaction detected (PLIP) MG.15: 1 residues within 4Å: Chain A: A.1311 No protein-ligand interaction detected (PLIP) MG.16: 2 residues within 4Å: Chain A: A.1012, G.1013 No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Chain A: A.1145, A.1146 No protein-ligand interaction detected (PLIP) MG.18: 3 residues within 4Å: Chain A: C.1054, A.1197, G.1198 No protein-ligand interaction detected (PLIP) MG.19: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.20: 2 residues within 4Å: Chain A: U.1189, G.1190 No protein-ligand interaction detected (PLIP) MG.21: 3 residues within 4Å: Chain A: G.993, U.1040, G.1041 No protein-ligand interaction detected (PLIP) MG.22: 3 residues within 4Å: Chain A: U.1083, G.1084, U.1085 No protein-ligand interaction detected (PLIP) MG.23: 2 residues within 4Å: Chain A: A.1067, A.1092 No protein-ligand interaction detected (PLIP) MG.24: 2 residues within 4Å: Chain A: C.1158, G.1184 No protein-ligand interaction detected (PLIP) MG.25: 2 residues within 4Å: Chain A: A.1167, U.1168 No protein-ligand interaction detected (PLIP) MG.26: 1 residues within 4Å: Chain A: G.1355 No protein-ligand interaction detected (PLIP) MG.27: 3 residues within 4Å: Chain A: C.980, A.1219, G.1220 No protein-ligand interaction detected (PLIP) MG.28: 2 residues within 4Å: Chain A: U.1235, C.1352 No protein-ligand interaction detected (PLIP) MG.29: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.31: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.32: 1 residues within 4Å: Chain I: S.58 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.30: 5 residues within 4Å: Chain C: H.18, D.188, N.203, D.204, D.205 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.18, C:D.188, C:D.204, C:D.205

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schedlbauer, A. et al., A binding site for the antibiotic GE81112 in the ribosomal mRNA channel. bioRxiv (2024)

Release Date

2025-08-06

Peptides

Small ribosomal subunit protein uS2: C
Small ribosomal subunit protein uS3: D
Small ribosomal subunit protein uS7: E
Small ribosomal subunit protein uS9: F
Small ribosomal subunit protein uS10: G
Small ribosomal subunit protein uS13: H
Small ribosomal subunit protein uS14: I
Small ribosomal subunit protein uS19: J

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
B

D
C

E
G

F
I

G
J

H
M

I
N

J
S

Small ribosomal subunit protein uS2

Small ribosomal subunit protein uS3

Small ribosomal subunit protein uS7

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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