SMTL ID : 6pwz.2 (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: 8 residues within 4Å: Chain A: G.28, T.29, A.30, S.31, G.32, K.33, S.34, R.169 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:A.30, A:S.31, A:G.32, A:K.33, A:S.34 Salt bridges: A:K.33, A:R.169 PO4.5: 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, B:S.35 Salt bridges: B:K.33, B:R.169 PO4.10: 8 residues within 4Å: Chain C: G.28, T.29, A.30, S.31, G.32, K.33, S.34, R.169 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:G.28, C:A.30, C:S.31, C:G.32, C:K.33, C:S.34 Water bridges: C:S.35, C:S.35 Salt bridges: C:K.33, C:R.169 PO4.17: 7 residues within 4Å: Chain D: G.28, A.30, S.31, G.32, K.33, S.34, R.169 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:A.30, D:S.31, D:G.32, D:K.33, D:S.34 Water bridges: D:K.33, D:K.33 Salt bridges: D:K.33, D:R.169

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: D.156, D.158, P.209 Chain D: K.201 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.158, A:P.209 Water bridges: A:D.158 GOL.3: 5 residues within 4Å: Chain A: S.164, L.168 Chain B: E.179, L.182, S.183 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.164, A:S.164, B:E.179, B:E.179 GOL.4: 2 residues within 4Å: Chain A: L.68, S.70 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.70 GOL.6: 8 residues within 4Å: Chain B: Q.61, P.86, F.89, N.91, I.94, L.138, Y.141, S.142 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.61, B:P.86, B:S.142, B:S.142 GOL.7: 5 residues within 4Å: Chain B: L.43, N.219, V.222, Q.223, Q.226 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.226 GOL.8: 3 residues within 4Å: Chain A: S.183 Chain B: S.164, R.165 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.164, B:R.165 GOL.9: 6 residues within 4Å: Chain B: T.29, D.62, Y.65, D.84, F.89, I.137 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.62 GOL.11: 4 residues within 4Å: Chain C: Y.141, R.146, K.202, Y.203 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.141, C:R.146, C:K.202, C:K.202 GOL.12: 5 residues within 4Å: Chain C: D.156, D.158, A.159, L.198, K.201 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.158, C:D.158, C:A.159, C:K.201 GOL.13: 7 residues within 4Å: Chain C: Q.61, P.86, F.89, N.91, I.94, L.138, Y.141 No protein-ligand interaction detected (PLIP) GOL.14: 3 residues within 4Å: Chain C: N.91, Y.141, Q.143 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.91 GOL.15: 3 residues within 4Å: Chain C: H.85, D.87, Y.141 No protein-ligand interaction detected (PLIP) GOL.18: 5 residues within 4Å: Chain D: D.156, T.157, D.158, P.209, R.210 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.158, D:D.158, D:R.210 GOL.19: 2 residues within 4Å: Chain D: S.142, E.144 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.142, D:E.144

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

P6D.16: 6 residues within 4Å: Chain C: Y.65, A.76, D.84, F.114, R.174, Q.184 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:D.62, C:Y.65, C:A.76, C:D.84, C:R.174 pi-Stacking: C:F.83 P6D.20: 8 residues within 4Å: Chain D: D.62, Y.65, F.83, D.84, I.137, R.166, R.174, Q.184 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.65, D:R.166, D:Q.184

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
B

B
C

C
E

D
H

Uridine-cytidine kinase 2

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