SMTL ID : 6n55.2 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.09 Å

Oligo State

homo-tetramer

Ligands

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

PO4.1: 8 residues within 4Å: Chain A: G.33, T.34, A.35, S.36, G.37, K.38, S.39, R.174 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:A.35, A:S.36, A:G.37, A:K.38, A:S.39 Water bridges: A:S.39 Salt bridges: A:K.38, A:R.174 PO4.5: 8 residues within 4Å: Chain B: G.33, T.34, A.35, S.36, G.37, K.38, S.39, R.174 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:A.35, B:S.36, B:G.37, B:K.38, B:S.39, B:S.39 Salt bridges: B:K.38, B:R.174 PO4.11: 8 residues within 4Å: Chain C: G.33, T.34, A.35, S.36, G.37, K.38, S.39, R.174 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:A.35, C:S.36, C:G.37, C:K.38, C:S.39 Salt bridges: C:K.38, C:R.174 PO4.13: 8 residues within 4Å: Chain D: G.33, T.34, A.35, S.36, G.37, K.38, S.39, R.174 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:A.35, D:S.36, D:G.37, D:K.38, D:S.39 Salt bridges: D:K.38, D:R.174

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: F.86, N.87, H.90, D.92 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.87, A:D.92 GOL.3: 4 residues within 4Å: Chain A: P.204, K.207, Y.208 Chain B: E.200 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.207, B:E.200 GOL.4: 4 residues within 4Å: Chain A: Y.70, Y.117, S.121, S.123 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.116, A:Y.117, A:S.123 GOL.6: 5 residues within 4Å: Chain B: D.161, D.163 Chain D: K.206, K.207, I.212 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.161, B:D.163 GOL.7: 3 residues within 4Å: Chain B: S.188, I.191 Chain C: S.169 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.169 GOL.8: 7 residues within 4Å: Chain A: E.200 Chain B: Y.146, R.151, P.204, T.205, K.207, Y.208 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.146, B:R.151, B:K.207, B:Y.208, A:E.200 GOL.9: 6 residues within 4Å: Chain B: Q.66, P.91, N.96, I.99, L.143, S.147 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.91, B:N.96, B:A.144 GOL.12: 5 residues within 4Å: Chain B: S.169, L.173 Chain C: L.187, S.188, I.191 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.187 GOL.14: 7 residues within 4Å: Chain A: A.164, K.195, F.198, E.199 Chain D: D.163, A.164, D.165 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:A.164 GOL.15: 7 residues within 4Å: Chain D: Q.66, P.91, F.94, N.96, I.99, L.143, S.147 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.66, D:P.91, D:S.147 GOL.16: 4 residues within 4Å: Chain D: Q.58, Q.60, P.133, D.135 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.58, D:Q.58, D:P.133 GOL.17: 2 residues within 4Å: Chain B: G.236 Chain D: D.232 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.232 GOL.18: 1 residues within 4Å: Chain D: R.174 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.174, D:R.174 GOL.19: 5 residues within 4Å: Chain D: L.98, K.101, E.105, V.112, Q.113 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.113

2 x UZ0: 2'-azido-2'-deoxyuridine(Covalent)(Non-covalent)

UZ0.10: 4 residues within 4Å: Chain B: Y.70, F.88, F.119, R.179 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.179, B:R.179 pi-Stacking: B:F.88 UZ0.20: 11 residues within 4Å: Chain D: T.34, Y.70, F.86, N.87, F.88, D.89, F.119, R.171, Q.189, F.193, V.194 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.88 Hydrogen bonds: D:F.88, D:R.171

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nainar, S. et al., An optimized chemical-genetic method for cell-specific metabolic labeling of RNA. Nat.Methods (2020)

Release Date

2019-11-27

Peptides

Uridine-cytidine kinase 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
E

C
G

D
D

Uridine-cytidine kinase 2

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