SMTL ID : 5c3z.1

Crystal structure of human ribokinase in complex with AMPPCP in C2 spacegroup

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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, G.237, A.238, G.240, T.256, V.259, T.264, A.267, G.268, F.271, N.295, A.298, A.299, V.302 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.199, A:G.237, A:T.264, A:G.266, A:A.267, A:G.268, A:N.295 Water bridges: A:T.235, A:V.259, A:T.264 ACP.6: 15 residues within 4Å: Chain B: N.199, T.235, G.237, A.238, G.240, T.256, V.259, T.264, A.267, G.268, F.271, N.295, A.298, A.299, V.302 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:N.199, B:G.237, B:T.264, B:A.267, B:G.268, B:N.295 Water bridges: B:A.238, B:A.238, B:V.259, B:D.269

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

NA.2: 7 residues within 4Å: Chain A: D.263, T.265, S.301, V.302, A.304, G.306, S.310 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.310, A:S.310 NA.3: 0 residues within 4Å: (No contacts) 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.54 Water bridges: A:N.177, A:D.269 NA.7: 6 residues within 4Å: Chain B: D.263, T.265, S.301, V.302, A.304, S.310 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.301, B:S.310 NA.8: 1 residues within 4Å: Chain B: G.268 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.54 Water bridges: B:G.268

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 4 residues within 4Å: Chain A: S.33, H.43, G.44, H.45 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: I.182, D.186, F.189 Ligand excluded by PLIP CL.9: 1 residues within 4Å: Chain B: R.168 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, J. et al., Crystal structure of human ribokinase in complex with AMPPCP in C2 spacegroup. 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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