SMTL ID : 4xck.1 (1 other biounit)

Vibrio cholerae O395 Ribokinase complexed with ADP, Ribose and Cesium ion.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.37 Å

Oligo State

homo-dimer

Ligands

1 x RIB: alpha-D-ribofuranose(Non-covalent)

RIB.1: 14 residues within 4Å: Chain A: N.14, D.16, G.41, G.42, K.43, N.46, A.98, I.110, I.112, E.143, T.251, A.252, D.255, A.291 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.14, A:D.16, A:G.42, A:K.43, A:N.46, A:E.143, A:A.252 Water bridges: A:D.255, A:D.255 Salt bridges: A:K.43

3 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 13 residues within 4Å: Chain A: T.223, G.225, S.226, F.243, V.245, T.250, A.253, G.254, F.257, H.279, A.282, A.283, V.286 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:T.223, A:G.225, A:V.245, A:V.245, A:T.250, A:T.250, A:G.254, A:H.279 Water bridges: A:A.253, A:A.283, A:A.283 ADP.4: 17 residues within 4Å: Chain B: N.187, T.223, L.224, G.225, S.226, V.229, F.243, V.245, A.247, T.250, A.253, G.254, F.257, H.279, A.282, V.286 Ligands: ADP.5 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.187, B:T.223, B:G.225, B:T.250, B:G.254, B:H.279 Water bridges: B:T.251, B:D.255 ADP.5: 16 residues within 4Å: Chain A: T.30 Chain B: N.14, D.16, G.41, G.42, K.43, N.46, A.98, I.110, I.112, E.143, T.250, T.251, D.255, A.291 Ligands: ADP.4 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.14, B:D.16, B:G.42, B:K.43, B:K.43, B:N.46, B:N.46, A:T.30 Water bridges: B:N.187, B:G.254, A:T.30 Salt bridges: B:K.43

2 x CS: CESIUM ION(Non-covalent)

CS.3: 6 residues within 4Å: Chain A: D.249, T.251, S.285, R.288, G.290, S.294 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.249, A:T.251, A:R.288 CS.6: 7 residues within 4Å: Chain B: D.249, T.251, A.252, S.285, R.288, G.290, S.294 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.249, B:R.288, H2O.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Paul, R. et al., Crystal Structure of Apo and Ligand Bound Vibrio cholerae Ribokinase (Vc-RK): Role of Monovalent Cation Induced Activation and Structural Flexibility in Sugar Phosphorylation. Adv. Exp. Med. Biol. (2015)

Release Date

2015-01-21

Peptides

Ribokinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribokinase

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