SMTL ID : 1xrj.1

Rapid structure determination of human uridine-cytidine kinase 2 using a conventional laboratory X-ray source and a single samarium derivative

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: S.34, R.169 Ligands: C5P.2, ADP.3 4 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: A:S.34, C5P.2, H2O.3, H2O.6 MG.4: 4 residues within 4Å: Chain B: S.34, S.60, D.62, E.135 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.62, B:E.135, H2O.15, H2O.15, H2O.15 MG.7: 4 residues within 4Å: Chain C: S.34, R.169 Ligands: C5P.8, ADP.9 4 PLIP interactions: 1 interactions with chain C, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: C:S.34, C5P.8, H2O.18, H2O.21 MG.10: 4 residues within 4Å: Chain D: S.34, S.60, D.62, E.135 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.62, D:E.135, H2O.29, H2O.29, H2O.29

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

C5P.2: 19 residues within 4Å: Chain A: T.29, A.30, K.33, D.62, Y.65, F.83, D.84, Y.112, F.114, H.117, I.137, R.166, R.169, R.174, R.176, Q.184, V.189 Ligands: MG.1, ADP.3 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:Y.65, A:F.83, A:Y.112 Hydrogen bonds: A:T.29, A:T.29, A:A.30, A:D.84, A:Y.112, A:H.117, A:R.166, A:R.166, A:R.174, A:R.176, A:R.176, A:Q.184 Water bridges: A:K.33, A:F.83, A:R.169, A:R.174 Salt bridges: A:K.33, A:R.169, A:R.174 pi-Stacking: A:F.83, A:F.114 C5P.5: 17 residues within 4Å: Chain B: T.29, A.30, K.33, Y.65, F.83, D.84, Y.112, F.114, H.117, I.137, R.166, R.169, R.174, R.176, Q.184, V.189 Ligands: ADP.6 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:Y.65, B:F.83, B:Y.112 Hydrogen bonds: B:T.29, B:T.29, B:A.30, B:Y.65, B:D.84, B:Y.112, B:Y.112, B:R.166, B:R.166, B:R.174, B:R.176, B:R.176, B:Q.184 Water bridges: B:K.33, B:S.34, B:F.83, B:R.169, B:R.169, B:D.170, B:R.174 Salt bridges: B:K.33, B:R.169, B:R.174 pi-Stacking: B:F.83, B:F.114 C5P.8: 19 residues within 4Å: Chain C: T.29, A.30, K.33, D.62, Y.65, F.83, D.84, Y.112, F.114, H.117, I.137, R.166, R.169, R.174, R.176, Q.184, V.189 Ligands: MG.7, ADP.9 26 PLIP interactions: 26 interactions with chain C Hydrophobic interactions: C:Y.65, C:F.83, C:Y.112 Hydrogen bonds: C:T.29, C:T.29, C:A.30, C:Y.65, C:D.84, C:Y.112, C:Y.112, C:R.166, C:R.166, C:R.174, C:R.176, C:R.176, C:Q.184 Water bridges: C:K.33, C:F.83, C:R.169, C:D.170, C:R.174 Salt bridges: C:K.33, C:R.169, C:R.174 pi-Stacking: C:F.83, C:F.114 C5P.11: 17 residues within 4Å: Chain D: T.29, A.30, K.33, Y.65, F.83, D.84, Y.112, F.114, H.117, I.137, R.166, R.169, R.174, R.176, Q.184, V.189 Ligands: ADP.12 27 PLIP interactions: 27 interactions with chain D Hydrophobic interactions: D:Y.65, D:F.83, D:Y.112 Hydrogen bonds: D:T.29, D:T.29, D:A.30, D:D.84, D:Y.112, D:H.117, D:R.166, D:R.166, D:R.174, D:R.176, D:R.176, D:Q.184 Water bridges: D:S.34, D:D.62, D:D.62, D:F.83, D:R.169, D:R.169, D:R.174 Salt bridges: D:K.33, D:R.169, D:R.174 pi-Stacking: D:F.83, D:F.114

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

ADP.3: 12 residues within 4Å: Chain A: G.28, A.30, S.31, G.32, K.33, S.34, S.35, R.165, R.169, D.213 Ligands: MG.1, C5P.2 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:A.30, A:S.31, A:G.32, A:K.33, A:S.34, A:S.34, A:S.35, A:R.169, A:D.213 Water bridges: A:K.33, A:S.34, A:R.165, A:R.165, A:R.169, A:D.213 Salt bridges: A:K.33 pi-Cation interactions: A:R.165 ADP.6: 12 residues within 4Å: Chain B: G.28, A.30, S.31, G.32, K.33, S.34, S.35, R.165, R.169, E.173, D.213 Ligands: C5P.5 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:A.30, B:S.31, B:G.32, B:K.33, B:S.34, B:S.34, B:S.35, B:R.169, B:D.213 Water bridges: B:K.33, B:K.33, B:S.34, B:S.34, B:R.165, B:R.165, B:R.165, B:R.169 Salt bridges: B:K.33 pi-Cation interactions: B:R.165, B:R.165 ADP.9: 12 residues within 4Å: Chain C: G.28, A.30, S.31, G.32, K.33, S.34, S.35, R.165, R.169, D.213 Ligands: MG.7, C5P.8 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:A.30, C:S.31, C:G.32, C:K.33, C:S.34, C:S.34, C:S.35, C:R.169, C:D.213 Water bridges: C:K.33, C:S.34, C:R.165, C:R.165, C:R.169, C:D.213 Salt bridges: C:K.33 pi-Cation interactions: C:R.165 ADP.12: 12 residues within 4Å: Chain D: G.28, A.30, S.31, G.32, K.33, S.34, S.35, R.165, R.169, E.173, D.213 Ligands: C5P.11 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:A.30, D:S.31, D:G.32, D:K.33, D:S.34, D:S.34, D:S.35, D:R.169, D:D.213 Water bridges: D:K.33, D:K.33, D:S.34, D:S.34, D:R.165, D:R.165, D:R.169, D:D.213 Salt bridges: D:K.33 pi-Cation interactions: D:R.165, D:R.165

Links

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Citation

Appleby, T.C. et al., Structure of human uridine-cytidine kinase 2 determined by SIRAS using a rotating-anode X-ray generator and a single samarium derivative. Acta Crystallogr.,Sect.D (2005)

Release Date

2005-03-15

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