SMTL ID : 6pwz.1 (1 other biounit)

Crystal structure of human uridine-cytidine kinase 2 complexed with 2'-azidocytidine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-tetramer

Ligands

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 7 residues within 4Å: Chain A: G.28, A.30, S.31, G.32, K.33, S.34, R.169 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.28, A:A.30, A:S.31, A:G.32, A:K.33, A:S.34 Water bridges: A:K.33, A:K.33 Salt bridges: A:K.33, A:R.169 PO4.8: 8 residues within 4Å: Chain B: G.28, T.29, A.30, S.31, G.32, K.33, S.34, R.169 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.28, B:A.30, B:S.31, B:G.32, B:K.33, B:S.34 Water bridges: B:K.33 Salt bridges: B:K.33, B:R.169 PO4.16: 8 residues within 4Å: Chain C: G.28, T.29, A.30, S.31, G.32, K.33, S.34, R.169 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:G.28, C:A.30, C:G.32, C:K.33, C:S.34 Salt bridges: C:K.33, C:R.169 PO4.20: 7 residues within 4Å: Chain D: G.28, A.30, S.31, G.32, K.33, S.34, R.169 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:A.30, D:S.31, D:S.31, D:G.32, D:K.33, D:S.34 Salt bridges: D:K.33, D:R.169

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: Y.141, R.146, T.200, K.202, Y.203 Ligand excluded by PLIP GOL.3: 4 residues within 4Å: Chain A: D.156, T.157, D.158, P.209 Ligand excluded by PLIP GOL.4: 4 residues within 4Å: Chain A: F.81, N.82, H.85, D.87 Ligand excluded by PLIP GOL.5: 7 residues within 4Å: Chain A: Q.61, P.86, N.91, I.94, L.138, S.142, V.145 Ligand excluded by PLIP GOL.6: 5 residues within 4Å: Chain A: F.81, F.83, D.84, Q.184, F.188 Ligand excluded by PLIP GOL.7: 6 residues within 4Å: Chain A: S.63, Y.65, V.67, D.90, L.93, P.110 Ligand excluded by PLIP GOL.9: 8 residues within 4Å: Chain B: Q.61, P.86, F.89, N.91, I.94, L.138, A.139, Y.141 Ligand excluded by PLIP GOL.10: 6 residues within 4Å: Chain B: I.58, L.59, S.60, S.63, I.109, V.126 Ligand excluded by PLIP GOL.11: 8 residues within 4Å: Chain B: F.81, N.82, F.83, D.84, R.166, Q.184, F.188 Ligands: P6D.15 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain B: K.96, E.100, V.107, Q.108 Ligand excluded by PLIP GOL.13: 5 residues within 4Å: Chain B: L.182, S.183, I.186 Chain D: S.164, L.168 Ligand excluded by PLIP GOL.14: 6 residues within 4Å: Chain B: D.156, A.159, R.162, F.193, L.198, K.201 Ligand excluded by PLIP GOL.17: 3 residues within 4Å: Chain C: L.93, K.96, E.100 Ligand excluded by PLIP GOL.18: 3 residues within 4Å: Chain B: R.210 Chain C: K.202, Y.203 Ligand excluded by PLIP GOL.19: 1 residues within 4Å: Chain C: R.119 Ligand excluded by PLIP GOL.21: 2 residues within 4Å: Chain D: S.35, R.169 Ligand excluded by PLIP

1 x P6D: 2'-azidocytidine(Non-covalent)

P6D.15: 5 residues within 4Å: Chain B: D.62, Y.65, F.83, R.174 Ligands: GOL.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.174, B:R.174 pi-Stacking: B:F.83 pi-Cation interactions: B:R.174

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nainar, S. et al., Incorporation of novel azido-nucleotides into RNA. To Be Published

Release Date

2020-07-29

Peptides

Uridine-cytidine kinase 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
F

D
G

Uridine-cytidine kinase 2

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