SMTL ID : 2fv7.1 (1 other biounit)

Crystal structure of human ribokinase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 4 residues within 4Å: Chain A: D.272, S.310, A.313, S.319 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.310, A:S.319 NA.10: 6 residues within 4Å: Chain B: D.272, T.274, S.310, V.311, A.313, S.319 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.313, B:S.319

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: G.277 Ligands: ADP.3 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain B: G.277 Ligands: ADP.12 No protein-ligand interaction detected (PLIP)

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.3: 18 residues within 4Å: Chain A: N.208, T.244, L.245, G.246, A.247, G.249, T.265, E.266, V.268, A.270, T.273, A.276, G.277, N.304, A.307, A.308, V.311 Ligands: MG.2 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:N.208, A:T.244, A:L.245, A:G.246, A:T.265, A:A.276, A:G.277, A:N.304 Water bridges: A:N.208, A:E.211, A:T.244, A:D.278, A:D.278 ADP.12: 17 residues within 4Å: Chain B: N.208, T.244, L.245, G.246, A.247, G.249, T.265, E.266, V.268, A.270, A.276, G.277, N.304, A.307, A.308, V.311 Ligands: MG.11 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.208, B:T.244, B:G.246, B:T.265, B:A.276, B:G.277, B:N.304 Water bridges: B:N.208, B:D.278

12 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.4: 6 residues within 4Å: Chain A: V.30, G.31, C.160, Q.161, I.164, S.169 No protein-ligand interaction detected (PLIP) UNX.5: 2 residues within 4Å: Chain A: K.182, D.203 No protein-ligand interaction detected (PLIP) UNX.6: 2 residues within 4Å: Chain A: G.180 Chain B: K.55 No protein-ligand interaction detected (PLIP) UNX.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) UNX.8: 2 residues within 4Å: Chain A: K.63, D.278 No protein-ligand interaction detected (PLIP) UNX.9: 1 residues within 4Å: Chain A: G.315 No protein-ligand interaction detected (PLIP) UNX.13: 6 residues within 4Å: Chain B: V.30, G.31, C.160, Q.161, I.164, S.169 No protein-ligand interaction detected (PLIP) UNX.14: 4 residues within 4Å: Chain B: G.61, G.62, N.66, T.316 No protein-ligand interaction detected (PLIP) UNX.15: 2 residues within 4Å: Chain B: K.182, V.240 No protein-ligand interaction detected (PLIP) UNX.16: 1 residues within 4Å: Chain B: D.87 No protein-ligand interaction detected (PLIP) UNX.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) UNX.18: 2 residues within 4Å: Chain B: G.59, F.60 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rabeh, W.M. et al., Crystal structure of human ribokinase. to be published

Release Date

2006-02-28

Peptides

Ribokinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribokinase

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