SMTL ID : 9cva.1

Crystal structure of human ribokinase in complex with K+, Mg2+, and AMPCP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: D.27, G.52, G.53, K.54, N.57, A.109, I.111, E.154 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.27, A:G.53, A:N.57, A:E.154 Water bridges: A:K.54

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

A12.2: 15 residues within 4Å: Chain A: N.199, T.235, L.236, G.237, A.238, G.240, T.256, V.259, A.267, G.268, N.295, A.298, A.299, V.302 Ligands: MG.5 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.199, A:T.235, A:L.236, A:G.237, A:T.256, A:N.295 Water bridges: A:N.199, A:E.200, A:E.200 A12.10: 16 residues within 4Å: Chain B: N.199, T.235, L.236, G.237, A.238, G.240, T.256, V.259, T.264, A.267, G.268, N.295, A.298, A.299, V.302 Ligands: MG.13 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:N.199, B:T.235, B:L.236, B:G.237, B:A.267, B:G.268, B:N.295 Water bridges: B:T.264, B:G.266, B:G.266, B:D.269

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 7 residues within 4Å: Chain A: K.173, D.194, V.231, L.279, P.283, L.287, M.290 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.173, A:P.283 PEG.7: 3 residues within 4Å: Chain B: K.173, D.194, V.231 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.173 PEG.8: 4 residues within 4Å: Chain B: G.66, Y.281, Y.282, E.324 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.66, B:E.324 PEG.9: 3 residues within 4Å: Chain B: E.204, G.208, L.209 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.204, B:E.204

2 x K: POTASSIUM ION(Non-covalent)

K.4: 6 residues within 4Å: Chain A: D.263, T.265, S.301, A.304, G.306, S.310 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.263, A:A.304, A:G.306, A:S.310, H2O.4 K.11: 6 residues within 4Å: Chain B: D.263, T.265, S.301, A.304, G.306, S.310 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.263, B:A.304, B:G.306, B:S.310, H2O.14

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

MG.5: 1 residues within 4Å: Ligands: A12.2 No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Ligands: A12.10 No protein-ligand interaction detected (PLIP)

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.6: 6 residues within 4Å: Chain B: I.49, F.51, D.83, E.86, N.87, Q.90 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.90

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

CL.12: 2 residues within 4Å: Chain B: S.33, H.45 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Akanmori, N.N. et al., Crystal structure of human ribokinase in complex with K+, Mg2+, and AMPCP. To Be Published

Release Date

2025-08-13

Peptides

Ribokinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribokinase

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