SMTL ID : 5c41.1 (1 other biounit)

Crystal structure of human ribokinase in complex with AMPPCP in P21 spacegroup and with 4 protomers

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

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

ACP.1: 15 residues within 4Å: Chain A: N.199, T.235, L.236, G.237, A.238, G.240, V.259, A.267, G.268, F.271, N.295, A.298, A.299, V.302 Ligands: NA.3 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:N.199, A:T.235, A:L.236, A:G.237, A:A.267, A:G.268, A:N.295 Water bridges: A:K.54, A:K.54, A:N.199, A:S.201, A:E.202, A:V.259, A:G.266, A:D.269 ACP.4: 19 residues within 4Å: Chain B: N.199, T.235, G.237, A.238, G.240, T.256, E.257, V.259, A.261, T.264, T.265, G.266, A.267, G.268, F.271, N.295, A.298, A.299, V.302 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:N.199, B:T.235, B:G.237, B:T.256, B:T.264, B:G.266, B:G.268, B:N.295 Water bridges: B:N.119, B:N.119, B:N.119, B:V.259, B:D.263, B:D.269

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

NA.2: 5 residues within 4Å: Chain A: D.263, S.301, V.302, A.304, S.310 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.265, A:S.310 NA.3: 2 residues within 4Å: Chain A: G.268 Ligands: ACP.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.54 Water bridges: A:N.177 NA.5: 6 residues within 4Å: Chain B: D.263, S.301, V.302, A.304, G.306, S.310 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.263, B:S.310 NA.6: 1 residues within 4Å: Chain B: G.268 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.269

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, J. et al., Crystal structure of human ribokinase in complex with AMPPCP in P21 spacegroup and with 4 protomers. To Be Published

Release Date

2016-06-15

Peptides

Ribokinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribokinase

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