SMTL ID : 5agv.1 (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

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

NA.1: 1 residues within 4Å: Chain A: E.146 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.146, A:E.146 Water bridges: A:G.224 NA.7: 3 residues within 4Å: Chain A: D.329, Y.330 Ligands: CA.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.329, A:Y.330 NA.8: 2 residues within 4Å: Chain A: S.25, V.73 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.25 NA.9: 4 residues within 4Å: Chain A: L.50, T.59, S.61, E.70 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.61, A:S.61, A:E.70 NA.10: 4 residues within 4Å: Chain A: G.298, N.340, P.341, T.342 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.342, A:T.342, A:T.342 Water bridges: A:N.340 NA.11: 2 residues within 4Å: Chain A: E.283, E.286 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.286 NA.15: 5 residues within 4Å: Chain C: H.273, L.368, R.370, A.390, V.391 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.370, C:V.391 NA.16: 1 residues within 4Å: Chain C: D.296 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.296 Water bridges: C:D.296 NA.17: 2 residues within 4Å: Chain C: A.218, S.253 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.253, C:S.253 NA.18: 5 residues within 4Å: Chain C: L.244, I.246, S.253, T.254, T.255 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:I.246, C:T.255, C:T.255 NA.19: 3 residues within 4Å: Chain C: R.88, L.89, D.92 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.92 NA.20: 1 residues within 4Å: Chain C: T.124 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.124

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

CA.2: 1 residues within 4Å: Ligands: NA.7 No protein-ligand interaction detected (PLIP) CA.3: 2 residues within 4Å: Chain A: T.393 Ligands: BU3.13 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.393, H2O.7, H2O.11, H2O.11, H2O.15 CA.4: 2 residues within 4Å: Chain A: N.383, G.384 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:N.383, A:G.384, H2O.7, H2O.8, H2O.10 CA.5: 4 residues within 4Å: Chain A: L.37, P.38, A.39 Ligands: BU3.12 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:L.37, A:A.39, H2O.2, H2O.4, H2O.6 CA.6: 3 residues within 4Å: Chain A: R.370, A.390, V.391 No protein-ligand interaction detected (PLIP) CA.14: 2 residues within 4Å: Chain C: T.393 Ligands: BU3.21 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:T.393, H2O.29, H2O.29, H2O.30, H2O.32

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

BU3.12: 6 residues within 4Å: Chain A: A.34, L.37, S.47, G.48, G.87 Ligands: CA.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.37 BU3.13: 8 residues within 4Å: Chain A: V.192, E.194, R.266, T.393, D.394, Y.395, V.396 Ligands: CA.3 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.396 Water bridges: A:T.393 BU3.21: 7 residues within 4Å: Chain C: V.192, E.194, T.393, D.394, Y.395, V.396 Ligands: CA.14 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:V.396 Hydrogen bonds: C:E.194, C:E.194 Water bridges: C:T.393 BU3.22: 7 residues within 4Å: Chain C: A.218, G.222, V.228, S.247, G.248, N.249, K.251 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:V.228, C:K.251 Hydrogen bonds: C:G.248, C:N.249 BU3.23: 5 residues within 4Å: Chain C: R.20, L.21, L.22, E.76, P.101 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.22, C:P.101 Hydrogen bonds: C:R.20, C:E.76 Water bridges: C:E.76

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
B

C
A

B
D

D
C

DNA POLYMERASE III SUBUNIT BETA

CYCLOHEXYL GRISELIMYCIN

Related Entries With Identical Sequence