SMTL ID : 5agv.2 (1 other biounit)

The sliding clamp of Mycobacterium tuberculosis in complex with a natural product.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

hetero-2-2-mer

Ligands

6 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.1: 2 residues within 4Å: Chain A: T.393 Ligands: BU3.8 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.393, H2O.9, H2O.9, H2O.10, H2O.13 CA.12: 1 residues within 4Å: Ligands: NA.17 No protein-ligand interaction detected (PLIP) CA.13: 2 residues within 4Å: Chain C: T.393 Ligands: BU3.23 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:T.393, H2O.25, H2O.28, H2O.29, H2O.33 CA.14: 2 residues within 4Å: Chain C: N.383, G.384 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:N.383, C:G.384, H2O.25, H2O.26, H2O.27 CA.15: 4 residues within 4Å: Chain C: L.37, P.38, A.39 Ligands: BU3.22 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:L.37, C:A.39, H2O.20, H2O.22, H2O.24 CA.16: 3 residues within 4Å: Chain C: R.370, A.390, V.391 No protein-ligand interaction detected (PLIP)

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

NA.2: 5 residues within 4Å: Chain A: H.273, L.368, R.370, A.390, V.391 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.273, A:V.391 NA.3: 1 residues within 4Å: Chain A: D.296 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.296 NA.4: 2 residues within 4Å: Chain A: A.218, S.253 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.253, A:S.253 NA.5: 5 residues within 4Å: Chain A: L.244, I.246, S.253, T.254, T.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.246, A:S.253 NA.6: 3 residues within 4Å: Chain A: R.88, L.89, D.92 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:D.92, C:L.293 NA.7: 1 residues within 4Å: Chain A: T.124 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.124 Water bridges: A:T.124 NA.11: 1 residues within 4Å: Chain C: E.146 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.146 Water bridges: C:G.224 NA.17: 3 residues within 4Å: Chain C: D.329, Y.330 Ligands: CA.12 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.329, C:Y.330, C:Y.330 NA.18: 2 residues within 4Å: Chain C: S.25, V.73 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.25 NA.19: 4 residues within 4Å: Chain C: L.50, T.59, S.61, E.70 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.61, C:E.70 NA.20: 4 residues within 4Å: Chain C: G.298, N.340, P.341, T.342 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.298, C:T.342 Water bridges: C:N.340 NA.21: 2 residues within 4Å: Chain C: E.283, E.286 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.286

5 x BU3: (R,R)-2,3-BUTANEDIOL(Non-covalent)

BU3.8: 7 residues within 4Å: Chain A: V.192, E.194, T.393, D.394, Y.395, V.396 Ligands: CA.1 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.396 Water bridges: A:T.393 BU3.9: 7 residues within 4Å: Chain A: A.218, G.222, V.228, S.247, G.248, N.249, K.251 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.228, A:K.251 Hydrogen bonds: A:G.248, A:N.249 BU3.10: 5 residues within 4Å: Chain A: R.20, L.21, L.22, E.76, P.101 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.22, A:P.101 Hydrogen bonds: A:R.20 Water bridges: A:E.76 BU3.22: 6 residues within 4Å: Chain C: A.34, L.37, S.47, G.48, G.87 Ligands: CA.15 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.37 BU3.23: 8 residues within 4Å: Chain C: V.192, E.194, R.266, T.393, D.394, Y.395, V.396 Ligands: CA.13 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.396 Hydrogen bonds: C:T.393 Water bridges: C:T.393

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kling, A. et al., Antibiotics. Targeting Dnan for Tuberculosis Therapy Using Novel Griselimycins. Science (2015)

Release Date

2015-06-03

Peptides

DNA POLYMERASE III SUBUNIT BETA: AC
CYCLOHEXYL GRISELIMYCIN: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

B
C

D
D

DNA POLYMERASE III SUBUNIT BETA

CYCLOHEXYL GRISELIMYCIN

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