SMTL ID : 9cvb.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 3 residues within 4Å: Chain A: I.49, F.51, D.83 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.83

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.2: 19 residues within 4Å: Chain A: K.54, N.199, E.200, T.235, L.236, G.237, A.238, G.240, V.259, G.266, A.267, G.268, D.269, F.271, N.295, A.298, A.299, V.302 Ligands: MG.3 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:N.199, A:T.235, A:G.237, A:G.266, A:G.268, A:D.269 Water bridges: A:K.54, A:K.54, A:K.54, A:K.54, A:N.177, A:N.199, A:T.256, A:A.267, A:A.267 ANP.6: 18 residues within 4Å: Chain B: K.54, N.199, T.235, L.236, G.237, A.238, G.240, V.259, T.264, G.266, A.267, G.268, D.269, N.295, A.298, A.299, V.302 Ligands: MG.8 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:K.54, B:N.199, B:T.235, B:T.235, B:L.236, B:G.237, B:G.266, B:G.268, B:D.269, B:D.269 Water bridges: B:K.54, B:K.54, B:K.54, B:N.177, B:N.177, B:N.177, B:N.199, B:V.259, B:A.267, B:A.267

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: G.268 Ligands: ANP.2 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain B: G.268 Ligands: ANP.6 No protein-ligand interaction detected (PLIP)

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.5 K.9: 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.15

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

PG4.5: 6 residues within 4Å: Chain B: I.49, F.51, D.83, E.86, N.87, Q.90 2 PLIP interactions: 2 interactions with chain B Water bridges: B:I.49, B:N.87 PG4.7: 3 residues within 4Å: Chain B: G.66, Y.281, Y.282 3 PLIP interactions: 3 interactions with chain B Water bridges: B:Y.281, B:Y.281, B:Y.282

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

CL.10: 5 residues within 4Å: Chain A: H.45 Chain B: V.124, A.125, G.126, L.129 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Akanmori, N.N. et al., To be published. To Be Published

Release Date

2025-08-06

Peptides

Ribokinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribokinase

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