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

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

Coordinates

PDB Format Compare

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 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.33, A:T.34, A:A.35, A:S.36, A:G.37, A:K.38, A:S.39 Salt bridges: A:K.38, A:R.174 PO4.6: 8 residues within 4Å: Chain B: G.33, T.34, A.35, S.36, G.37, K.38, S.39, R.174 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:A.35, B:S.36, B:S.36, B:G.37, B:K.38, B:S.39 Water bridges: 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, S.40 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, C:S.40 Salt bridges: C:K.38 PO4.18: 8 residues within 4Å: Chain D: G.33, T.34, A.35, S.36, G.37, K.38, S.39, R.174 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:A.35, D:S.36, D:S.36, D:G.37, D:K.38, D:S.39, D:S.39 Salt bridges: D:K.38, D:R.174

13 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: P.204, K.207, Y.208 Chain C: E.200 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.151, A:K.207, A:Y.208 Water bridges: A:R.151 GOL.3: 3 residues within 4Å: Chain A: S.169, L.173 Chain B: S.188 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.169 GOL.4: 7 residues within 4Å: Chain A: Q.66, N.96, I.99, L.143, Y.146, S.147, V.150 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.66 GOL.5: 4 residues within 4Å: Chain A: F.86, N.87, H.90, D.92 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.87, A:D.92, A:D.92 GOL.7: 4 residues within 4Å: Chain A: L.187, S.188, I.191 Chain B: L.173 No protein-ligand interaction detected (PLIP) GOL.8: 2 residues within 4Å: Chain B: P.133, D.135 No protein-ligand interaction detected (PLIP) GOL.9: 9 residues within 4Å: Chain B: Q.66, P.91, F.94, N.96, I.99, L.143, A.144, S.147, V.150 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.66, B:P.91, B:A.144, B:Y.146, B:S.147 GOL.10: 3 residues within 4Å: Chain B: K.207, Y.208 Chain C: R.215 No protein-ligand interaction detected (PLIP) GOL.12: 3 residues within 4Å: Chain C: E.105, E.108, K.110 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.105, C:K.110 GOL.13: 6 residues within 4Å: Chain C: E.184, L.187, S.188, I.191 Chain D: S.169, L.173 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.169, C:E.184 GOL.14: 9 residues within 4Å: Chain C: Q.66, P.91, F.94, N.96, I.99, L.143, A.144, Y.146, S.147 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:P.91, C:S.147 GOL.15: 5 residues within 4Å: Chain C: L.98, T.102, E.105, V.112, Q.113 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.113 GOL.16: 4 residues within 4Å: Chain C: K.104, T.107, E.108, L.153 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.108

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

UZ0.17: 5 residues within 4Å: Chain C: Y.70, F.88, D.89, F.119, R.179 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.88 Hydrogen bonds: C:D.89, C:R.179, C:R.179 pi-Cation interactions: C:R.179

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
A

B
C

C
F

D
H

Uridine-cytidine kinase 2

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