SMTL ID : 8cvo.1

Cutibacterium acnes 30S ribosomal subunit with Sarecycline bound, head domain only in the local refined map

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x V7A: Sarecycline(Non-functional Binders)

V7A.1: 7 residues within 4Å: Chain A: U.949, G.950, G.1038, C.1039, A.1183, G.1184 Ligands: MG.4 No protein-ligand interaction detected (PLIP)

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

MG.2: 2 residues within 4Å: Chain A: C.964 Chain H: A.20 No protein-ligand interaction detected (PLIP) MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain A: C.1039, A.1183, G.1184 Ligands: V7A.1 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain A: A.948, G.1184, U.1185 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain A: C.946, G.1036, C.1186 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain A: C.1039, A.1183, G.1184, U.1185 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain A: G.935, U.1210 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain A: A.921, G.923 No protein-ligand interaction detected (PLIP) MG.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain A: G.928, G.929, A.930 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain A: C.1094, A.1095, U.1175 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Chain A: C.918, U.1331 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.14: 4 residues within 4Å: Chain H: C.24, C.27, C.40, C.43 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.24, H:C.27, H:C.40, H:C.43

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lomakin, I.B. et al., Sarecycline inhibits protein translation in Cutibacterium acnes 70S ribosome using a two-site mechanism. Nucleic Acids Res. (2023)

Release Date

2023-03-15

Peptides

30S ribosomal protein S5: B
30S ribosomal protein S3: C
30S ribosomal protein S7: D
30S ribosomal protein S9: E
30S ribosomal protein S10: F
30S ribosomal protein S13: G
30S ribosomal protein S14 type Z: H
30S ribosomal protein S19: I

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
E

C
G

D
I

E
J

F
M

G
N

H
S

I
U

30S ribosomal protein S5

30S ribosomal protein S3

30S ribosomal protein S7

30S ribosomal protein S9

30S ribosomal protein S10

30S ribosomal protein S13

30S ribosomal protein S14 type Z

30S ribosomal protein S19

Related Entries With Identical Sequence