SMTL ID : 3go6.2 (1 other biounit)

Crystal Structure of M. tuberculosis ribokinase (Rv2436) in complex with ribose and AMP-PNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-tetramer

Ligands

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

RIB.1: 13 residues within 4Å: Chain A: N.29, D.31, G.56, G.57, K.58, N.61, A.112, I.114, V.124, V.126, E.152, D.248, V.288 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.29, A:D.31, A:G.57, A:K.58, A:K.58, A:N.61, A:E.152 Water bridges: A:G.245, A:G.245, A:D.248 Salt bridges: A:K.58 RIB.5: 13 residues within 4Å: Chain C: N.29, D.31, G.56, G.57, K.58, N.61, A.112, I.114, V.124, V.126, E.152, D.248, V.288 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:N.29, C:D.31, C:G.57, C:K.58, C:K.58, C:N.61, C:E.152 Water bridges: C:G.245, C:G.245, C:D.248 Salt bridges: C:K.58

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: D.242, A.244, A.282, V.285, G.287, C.291 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.242, A:A.244, A:A.282, A:V.285, A:G.287 MG.4: 6 residues within 4Å: Chain B: D.242, A.244, A.282, V.285, G.287, C.291 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.242, B:A.244, B:A.282, B:V.285, B:G.287 MG.6: 6 residues within 4Å: Chain C: D.242, A.244, A.282, V.285, G.287, C.291 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.242, C:A.244, C:A.282, C:V.285, C:G.287 MG.8: 6 residues within 4Å: Chain D: D.242, A.244, A.282, V.285, G.287, C.291 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.242, D:A.244, D:A.282, D:V.285, D:G.287

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

ADP.3: 17 residues within 4Å: Chain B: T.216, G.218, V.219, G.221, A.235, P.236, V.238, P.240, T.243, G.245, A.246, G.247, F.250, C.276, G.279, A.280, T.283 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:T.216, B:L.217, B:T.243, B:G.245, B:A.246, B:G.247, B:A.280 Water bridges: B:N.199, B:N.199, B:G.218, B:G.218, B:V.238, B:D.248 ADP.7: 17 residues within 4Å: Chain D: T.216, G.218, V.219, G.221, A.235, P.236, V.238, P.240, T.243, G.245, A.246, G.247, F.250, C.276, G.279, A.280, T.283 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:T.216, D:L.217, D:G.245, D:A.246, D:G.247, D:A.280 Water bridges: D:N.199, D:N.199, D:G.218, D:G.218, D:V.238, D:D.248

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Masters, E.I. et al., Crystal structure and biochemical characterization of M.tuberculosis ribokinase (Rv2436). To be Published

Release Date

2010-03-31

Peptides

RIBOKINASE RBSK: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

RIBOKINASE RBSK

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