SMTL ID : 8cix.1

DNA-polymerase sliding clamp (DnaN) from Escherichia coli in complex with Griselimycin.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

hetero-2-2-mer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: D.153, R.155, D.176, G.177, H.178 Chain B: T.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.155, A:D.176, A:H.178 Water bridges: A:D.153 GOL.21: 6 residues within 4Å: Chain C: D.153, R.155, D.176, G.177, H.178 Chain D: T.4 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.155, C:D.176, C:H.178 Water bridges: C:D.153

14 x CA: CALCIUM ION(Non-covalent)

CA.2: 2 residues within 4Å: Chain A: E.9, G.88 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.9, A:E.9, A:G.88, H2O.9, H2O.10 CA.3: 4 residues within 4Å: Chain A: T.50, L.52, E.55, P.120 No protein-ligand interaction detected (PLIP) CA.4: 3 residues within 4Å: Chain A: E.96 Ligands: ACT.9, ACT.10 4 PLIP interactions: 1 interactions with chain A, 2 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:E.96, ACT.9, ACT.10, H2O.10 CA.5: 4 residues within 4Å: Chain A: E.337, N.338, A.355, A.356 No protein-ligand interaction detected (PLIP) CA.6: 4 residues within 4Å: Chain A: P.245, D.246, R.249 Chain B: V.8 No protein-ligand interaction detected (PLIP) CA.7: 4 residues within 4Å: Chain A: N.121, L.122 Ligands: ACT.11, NA.17 5 PLIP interactions: 4 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: H2O.2, H2O.6, H2O.6, H2O.11, ACT.11 CA.8: 1 residues within 4Å: Chain A: E.337 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.337, A:E.337, H2O.8, H2O.8, H2O.11 CA.22: 2 residues within 4Å: Chain C: E.9, G.88 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.9, C:E.9, C:G.88, H2O.24, H2O.25 CA.23: 4 residues within 4Å: Chain C: T.50, L.52, E.55, P.120 No protein-ligand interaction detected (PLIP) CA.24: 3 residues within 4Å: Chain C: E.96 Ligands: ACT.29, ACT.30 4 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions, 2 Ligand-Ligand interactions Metal complexes: C:E.96, H2O.25, ACT.29, ACT.30 CA.25: 4 residues within 4Å: Chain C: E.337, N.338, A.355, A.356 No protein-ligand interaction detected (PLIP) CA.26: 4 residues within 4Å: Chain C: P.245, D.246, R.249 Chain D: V.8 No protein-ligand interaction detected (PLIP) CA.27: 4 residues within 4Å: Chain C: N.121, L.122 Ligands: ACT.31, NA.37 No protein-ligand interaction detected (PLIP) CA.28: 1 residues within 4Å: Chain C: E.337 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.337, C:E.337, H2O.22, H2O.23, H2O.25

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.9: 3 residues within 4Å: Chain A: E.96 Ligands: CA.4, ACT.10 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.97 ACT.10: 3 residues within 4Å: Chain A: E.96 Ligands: CA.4, ACT.9 No protein-ligand interaction detected (PLIP) ACT.11: 7 residues within 4Å: Chain A: E.55, V.57, R.227, I.234, T.236 Ligands: CA.7, NA.17 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.234 Water bridges: A:L.122, A:R.227, A:R.227, A:R.227, A:T.236 Salt bridges: A:R.227 ACT.29: 3 residues within 4Å: Chain C: E.96 Ligands: CA.24, ACT.30 1 PLIP interactions: 1 interactions with chain C Water bridges: C:G.97 ACT.30: 3 residues within 4Å: Chain C: E.96 Ligands: CA.24, ACT.29 No protein-ligand interaction detected (PLIP) ACT.31: 7 residues within 4Å: Chain C: E.55, V.57, R.227, I.234, T.236 Ligands: CA.27, NA.37 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:I.234 Water bridges: C:L.122, C:R.227, C:R.227, C:R.227, C:T.236 Salt bridges: C:R.227

8 x MG: MAGNESIUM ION(Non-covalent)

MG.12: 5 residues within 4Å: Chain A: R.3, M.4, G.69, A.70, L.95 No protein-ligand interaction detected (PLIP) MG.13: 4 residues within 4Å: Chain A: E.96, R.99, L.101, S.110 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.110, H2O.7 MG.14: 5 residues within 4Å: Chain A: N.35, P.74, S.112, T.113, L.114 No protein-ligand interaction detected (PLIP) MG.15: 1 residues within 4Å: Chain A: S.348 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.348, H2O.3, H2O.10 MG.32: 5 residues within 4Å: Chain C: R.3, M.4, G.69, A.70, L.95 No protein-ligand interaction detected (PLIP) MG.33: 4 residues within 4Å: Chain C: E.96, R.99, L.101, S.110 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:S.110, H2O.22 MG.34: 5 residues within 4Å: Chain C: N.35, P.74, S.112, T.113, L.114 No protein-ligand interaction detected (PLIP) MG.35: 1 residues within 4Å: Chain C: S.348 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.348, H2O.17, H2O.25

10 x NA: SODIUM ION(Non-functional Binders)

NA.16: 6 residues within 4Å: Chain A: H.229, V.230, G.231, D.232, F.233, I.234 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.230, A:G.231 Water bridges: A:G.231 NA.17: 5 residues within 4Å: Chain A: L.37, T.48, V.57 Ligands: CA.7, ACT.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.39 NA.18: 5 residues within 4Å: Chain A: E.90, A.92, R.103, S.104, G.105 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.92, A:R.103 Water bridges: A:G.105 NA.19: 3 residues within 4Å: Chain A: N.278, N.298, N.299 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.298 Water bridges: A:G.283, A:G.283, A:N.298 NA.20: 2 residues within 4Å: Chain A: G.2, R.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.3 Water bridges: A:R.3, A:R.3, A:L.95, A:L.95, A:L.95 NA.36: 6 residues within 4Å: Chain C: H.229, V.230, G.231, D.232, F.233, I.234 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.230, C:G.231 Water bridges: C:G.231 NA.37: 5 residues within 4Å: Chain C: L.37, T.48, V.57 Ligands: CA.27, ACT.31 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.39 NA.38: 5 residues within 4Å: Chain C: E.90, A.92, R.103, S.104, G.105 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.90, C:A.92 Water bridges: C:G.105 NA.39: 3 residues within 4Å: Chain C: N.278, N.298, N.299 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.298, C:N.298 Water bridges: C:G.283 NA.40: 2 residues within 4Å: Chain C: G.2, R.3 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.3, C:R.3 Water bridges: C:L.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fu, C. et al., Elucidation of unusual biosynthesis and DnaN-targeting mode of action of potent anti-tuberculosis antibiotics Mycoplanecins. Nat Commun (2024)

Release Date

2023-11-29

Peptides

Beta sliding clamp: AC
Griselimycin: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Beta sliding clamp

Griselimycin

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