SMTL ID : 6wjz.1

Crystal structure of human ribokinase in complex with AMPCP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x A12: PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)

A12.1: 17 residues within 4Å: Chain A: N.186, T.222, L.223, G.224, A.225, G.227, T.243, E.244, V.246, A.248, A.254, G.255, N.282, A.285, A.286, V.289 Ligands: MG.8 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:N.186, A:T.222, A:L.223, A:G.224, A:T.243, A:N.282 Water bridges: A:N.186, A:E.187, A:E.187, A:K.245, A:V.246, A:A.254 A12.9: 16 residues within 4Å: Chain B: N.186, T.222, L.223, G.224, A.225, G.227, T.243, E.244, V.246, A.254, G.255, N.282, A.285, A.286, V.289 Ligands: MG.12 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:N.186, B:T.222, B:G.224, B:T.251, B:A.254, B:G.255, B:N.282 Water bridges: B:V.246, B:G.253, B:D.256

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: D.14, G.39, G.40, K.41, N.44, A.96, I.98, E.141 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.14, A:G.40, A:N.44, A:E.141 GOL.3: 1 residues within 4Å: Chain A: E.83 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.83, A:E.83 GOL.4: 4 residues within 4Å: Chain A: K.61, T.88, N.119 Ligands: GOL.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.61, A:T.88, A:N.119 Water bridges: A:T.88 GOL.5: 7 residues within 4Å: Chain A: K.160, V.182, L.266, L.272, S.273, L.274, M.277 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.160, A:L.272 Water bridges: A:D.181, A:L.274 GOL.6: 3 residues within 4Å: Chain A: L.117, N.119 Ligands: GOL.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.117, A:N.119 GOL.10: 7 residues within 4Å: Chain B: D.14, G.39, G.40, K.41, N.44, A.96, E.141 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.14, B:G.40, B:N.44, B:E.141 Water bridges: B:D.256

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

NA.7: 6 residues within 4Å: Chain A: D.250, T.252, S.288, V.289, A.291, S.297 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.252, A:S.297 NA.11: 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:A.291, B:S.297

2 x MG: MAGNESIUM ION(Non-functional Binders)

MG.8: 1 residues within 4Å: Ligands: A12.1 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Ligands: A12.9 No protein-ligand interaction detected (PLIP)

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
A

B
B

Ribokinase

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