SMTL ID : 1uj2.1

Crystal structure of human uridine-cytidine kinase 2 complexed with products, CMP and ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: S.36 Ligands: C5P.2, ADP.3 5 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:S.36, H2O.1, H2O.7, H2O.9, C5P.2 MG.4: 3 residues within 4Å: Chain B: S.36 Ligands: C5P.5, ADP.6 5 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: B:S.36, C5P.5, H2O.13, H2O.16, H2O.18 MG.7: 3 residues within 4Å: Chain C: S.36 Ligands: C5P.8, ADP.9 5 PLIP interactions: 1 interactions with chain C, 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: C:S.36, C5P.8, H2O.18, H2O.24, H2O.26 MG.10: 3 residues within 4Å: Chain D: S.36 Ligands: C5P.11, ADP.12 5 PLIP interactions: 1 interactions with chain D, 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: D:S.36, C5P.11, H2O.30, H2O.33, H2O.35

4 x C5P: CYTIDINE-5'-MONOPHOSPHATE(Non-covalent)

C5P.2: 19 residues within 4Å: Chain A: T.31, A.32, K.35, D.64, Y.67, F.85, D.86, Y.114, F.116, H.119, I.139, R.168, R.171, R.176, R.178, Q.186, V.191 Ligands: MG.1, ADP.3 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:Y.67, A:F.85, A:Y.114 Hydrogen bonds: A:T.31, A:T.31, A:A.32, A:D.86, A:Y.114, A:H.119, A:R.168, A:R.168, A:R.176, A:R.178, A:R.178, A:Q.186 Water bridges: A:K.35, A:S.36, A:F.85, A:R.171, A:R.176 Salt bridges: A:K.35, A:R.171, A:R.176 pi-Stacking: A:F.85, A:F.116 C5P.5: 19 residues within 4Å: Chain B: T.31, A.32, K.35, D.64, Y.67, F.85, D.86, Y.114, F.116, H.119, I.139, R.168, R.171, R.176, R.178, Q.186, V.191 Ligands: MG.4, ADP.6 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:Y.67, B:F.85, B:Y.114 Hydrogen bonds: B:T.31, B:T.31, B:A.32, B:Y.67, B:D.86, B:Y.114, B:Y.114, B:R.168, B:R.168, B:R.176, B:R.178, B:R.178, B:Q.186 Water bridges: B:K.35, B:S.36, B:S.36, B:D.86, B:R.171, B:D.172 Salt bridges: B:K.35, B:R.171, B:R.176 pi-Stacking: B:F.85, B:F.116 C5P.8: 19 residues within 4Å: Chain C: T.31, A.32, K.35, D.64, Y.67, F.85, D.86, Y.114, F.116, H.119, I.139, R.168, R.171, R.176, R.178, Q.186, V.191 Ligands: MG.7, ADP.9 27 PLIP interactions: 27 interactions with chain C Hydrophobic interactions: C:Y.67, C:F.85, C:Y.114 Hydrogen bonds: C:T.31, C:T.31, C:A.32, C:Y.67, C:D.86, C:Y.114, C:Y.114, C:R.168, C:R.168, C:R.176, C:R.178, C:R.178, C:Q.186 Water bridges: C:K.35, C:S.36, C:F.85, C:R.171, C:D.172, C:R.176 Salt bridges: C:K.35, C:R.171, C:R.176 pi-Stacking: C:F.85, C:F.116 C5P.11: 19 residues within 4Å: Chain D: T.31, A.32, K.35, D.64, Y.67, F.85, D.86, Y.114, F.116, H.119, I.139, R.168, R.171, R.176, R.178, Q.186, V.191 Ligands: MG.10, ADP.12 25 PLIP interactions: 25 interactions with chain D Hydrophobic interactions: D:Y.67, D:F.85, D:Y.114 Hydrogen bonds: D:T.31, D:T.31, D:A.32, D:D.86, D:Y.114, D:H.119, D:R.168, D:R.168, D:R.176, D:R.178, D:R.178, D:Q.186 Water bridges: D:K.35, D:S.36, D:S.36, D:D.86, D:R.171 Salt bridges: D:K.35, D:R.171, D:R.176 pi-Stacking: D:F.85, D:F.116

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

ADP.3: 13 residues within 4Å: Chain A: G.30, A.32, S.33, G.34, K.35, S.36, S.37, R.167, R.171, R.212, D.215 Ligands: MG.1, C5P.2 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:A.32, A:S.33, A:G.34, A:K.35, A:S.36, A:S.36, A:S.37, A:R.171, A:D.215 Water bridges: A:K.35, A:K.35, A:S.36, A:S.36, A:R.171, A:E.175, A:E.175, A:A.214 Salt bridges: A:K.35 pi-Cation interactions: A:R.167, A:R.167 ADP.6: 12 residues within 4Å: Chain B: G.30, A.32, S.33, G.34, K.35, S.36, S.37, R.167, R.171, D.215 Ligands: MG.4, C5P.5 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:A.32, B:S.33, B:G.34, B:K.35, B:S.36, B:S.36, B:S.37, B:R.167, B:R.171, B:D.215 Water bridges: B:K.35, B:K.35, B:S.36, B:S.36, B:R.171 Salt bridges: B:K.35, B:R.171 pi-Cation interactions: B:R.167 ADP.9: 13 residues within 4Å: Chain C: G.30, A.32, S.33, G.34, K.35, S.36, S.37, R.167, R.171, R.212, D.215 Ligands: MG.7, C5P.8 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:A.32, C:S.33, C:G.34, C:K.35, C:S.36, C:S.36, C:S.37, C:R.171, C:D.215 Water bridges: C:K.35, C:K.35, C:S.36, C:S.36, C:R.171, C:E.175, C:E.175, C:A.214 Salt bridges: C:K.35 pi-Cation interactions: C:R.167, C:R.167 ADP.12: 12 residues within 4Å: Chain D: G.30, A.32, S.33, G.34, K.35, S.36, S.37, R.167, R.171, D.215 Ligands: MG.10, C5P.11 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:A.32, D:S.33, D:G.34, D:K.35, D:S.36, D:S.36, D:S.37, D:R.171, D:D.215 Water bridges: D:K.35, D:K.35, D:S.36, D:S.36, D:R.167, D:R.167, D:R.171, D:D.215 Salt bridges: D:K.35, D:R.171 pi-Cation interactions: D:R.167

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Suzuki, N.N. et al., Structural basis for the specificity, catalysis, and regulation of human uridine-cytidine kinase. STRUCTURE (2004)

Release Date

2004-05-04

Peptides

Uridine-cytidine kinase 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Uridine-cytidine kinase 2

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