SMTL ID : 8ciy.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

hetero-2-2-mer

Ligands

12 x CA: CALCIUM ION(Non-covalent)

CA.1: 2 residues within 4Å: Chain A: E.9, G.88 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.9, A:E.9, A:G.88, H2O.9 CA.2: 4 residues within 4Å: Chain A: E.337, N.338, A.355, A.356 No protein-ligand interaction detected (PLIP) CA.3: 2 residues within 4Å: Chain A: E.96 Ligands: GOL.14 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.96, H2O.11 CA.4: 5 residues within 4Å: Chain A: E.301, E.303 Chain C: P.74, K.77, S.112 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Metal complexes: C:S.112, A:E.303 CA.5: 2 residues within 4Å: Chain A: S.357, Q.358 No protein-ligand interaction detected (PLIP) CA.6: 3 residues within 4Å: Chain A: E.11, E.87, G.88 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.11, H2O.2 CA.16: 2 residues within 4Å: Chain C: E.9, G.88 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.9, C:E.9, C:G.88, H2O.25 CA.17: 4 residues within 4Å: Chain C: E.337, N.338, A.355, A.356 No protein-ligand interaction detected (PLIP) CA.18: 2 residues within 4Å: Chain C: E.96 Ligands: GOL.29 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.96, H2O.27 CA.19: 5 residues within 4Å: Chain A: P.74, K.77, S.112 Chain C: E.301, E.303 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Metal complexes: C:E.303, A:S.112 CA.20: 2 residues within 4Å: Chain C: S.357, Q.358 No protein-ligand interaction detected (PLIP) CA.21: 3 residues within 4Å: Chain C: E.11, E.87, G.88 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.11, H2O.18

10 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 1 residues within 4Å: Chain A: N.121 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain A: R.208, D.211 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:R.208, A:D.211, A:D.211, H2O.1 MG.9: 5 residues within 4Å: Chain A: R.243, P.245, D.246, R.249 Chain B: V.8 No protein-ligand interaction detected (PLIP) MG.10: 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.9 MG.11: 4 residues within 4Å: Chain A: S.348, S.349, M.365 Chain B: P.6 No protein-ligand interaction detected (PLIP) MG.22: 1 residues within 4Å: Chain C: N.121 No protein-ligand interaction detected (PLIP) MG.23: 2 residues within 4Å: Chain C: R.208, D.211 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:R.208, C:D.211, C:D.211, H2O.16 MG.24: 5 residues within 4Å: Chain C: R.243, P.245, D.246, R.249 Chain D: V.8 No protein-ligand interaction detected (PLIP) MG.25: 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.24 MG.26: 4 residues within 4Å: Chain C: S.348, S.349, M.365 Chain D: P.6 No protein-ligand interaction detected (PLIP)

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

NA.12: 3 residues within 4Å: Chain A: N.278, N.298, N.299 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.298, A:N.298 Water bridges: A:G.283 NA.27: 3 residues within 4Å: Chain C: N.278, N.298, N.299 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.298 Water bridges: C:G.283, C:G.283, C:N.298

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 6 residues within 4Å: Chain A: K.257, A.316, E.317, M.318, T.344, D.345 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.257, A:E.317 GOL.14: 2 residues within 4Å: Chain A: E.96 Ligands: CA.3 No protein-ligand interaction detected (PLIP) GOL.28: 6 residues within 4Å: Chain C: K.257, A.316, E.317, M.318, T.344, D.345 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.257, C:E.317 GOL.29: 2 residues within 4Å: Chain C: E.96 Ligands: CA.18 No protein-ligand interaction detected (PLIP)

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

ACT.15: 3 residues within 4Å: Chain A: K.253, N.254, P.255 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.254 ACT.30: 3 residues within 4Å: Chain C: K.253, N.254, P.255 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.254

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
Cyclohexyl-Griselimycin: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Beta sliding clamp

Cyclohexyl-Griselimycin

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