SMTL ID : 6wk0.2 (1 other biounit)

Crystal structure of human ribokinase in complex with AMPPCP and ribose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

RIB.1: 13 residues within 4Å: Chain A: M.12, D.14, G.39, G.40, K.41, N.44, A.96, I.110, E.141, T.252, G.253, D.256, T.294 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:D.14, A:G.40, A:K.41, A:K.41, A:N.44, A:E.141, A:G.253, A:T.294, A:T.294 Water bridges: A:K.41, A:T.251, A:D.256 Salt bridges: A:K.41

2 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.2: 18 residues within 4Å: Chain A: N.186, T.222, L.223, G.224, A.225, G.227, T.243, V.246, T.251, A.254, G.255, F.258, N.282, A.285, A.286, V.289 Chain B: G.26 Ligands: NA.4 20 PLIP interactions: 17 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.186, A:T.222, A:L.223, A:G.224, A:A.254, A:G.255, A:N.282, B:G.26 Water bridges: A:N.106, A:N.186, A:S.188, A:V.246, A:T.251, A:G.253, A:G.253, A:D.256, A:A.286, A:A.286, B:T.28, B:T.28 ACP.5: 17 residues within 4Å: Chain B: N.186, T.222, G.224, A.225, G.227, T.243, V.246, A.248, T.251, A.254, G.255, F.258, N.282, A.285, A.286, V.289 Ligands: NA.7 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:N.186, B:G.224, B:A.254, B:G.255, B:N.282 Water bridges: B:N.186, B:S.188, B:T.251, B:T.251, B:D.256

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

NA.3: 6 residues within 4Å: Chain A: D.250, T.252, S.288, A.291, G.293, S.297 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.288, A:S.297 NA.4: 3 residues within 4Å: Chain A: K.41, G.255 Ligands: ACP.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.189 Water bridges: A:D.256 NA.6: 6 residues within 4Å: Chain B: D.250, T.252, S.288, V.289, A.291, S.297 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.250, B:S.297 NA.7: 4 residues within 4Å: Chain B: K.41, N.186, G.255 Ligands: ACP.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.186

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, J., Crystal structures of human ribokinase. To Be Published

Release Date

2021-04-21

Peptides

Ribokinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Ribokinase

Related Entries With Identical Sequence