SMTL ID : 6n53.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

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

PO4.1: 9 residues within 4Å: Chain A: G.33, A.35, S.36, G.37, K.38, S.39, R.174 Ligands: MG.2, UZR.4 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.33, A:A.35, A:S.36, A:G.37, A:K.38, A:S.39, A:S.39 Salt bridges: A:K.38, A:R.174 PO4.5: 10 residues within 4Å: Chain B: G.33, A.35, S.36, G.37, K.38, S.39, E.140, R.174 Ligands: MG.6, UZR.11 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:A.35, B:S.36, B:G.37, B:K.38, B:S.39 Water bridges: B:G.37, B:S.39, B:S.40 Salt bridges: B:K.38, B:R.174 PO4.12: 9 residues within 4Å: Chain C: G.33, A.35, S.36, G.37, K.38, S.39, R.174 Ligands: MG.13, UZR.15 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:G.33, C:A.35, C:S.36, C:G.37, C:K.38, C:S.39, C:S.39 Salt bridges: C:K.38, C:R.174 PO4.16: 10 residues within 4Å: Chain D: G.33, A.35, S.36, G.37, K.38, S.39, E.140, R.174 Ligands: MG.17, UZR.22 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:A.35, D:S.36, D:G.37, D:K.38, D:S.39 Water bridges: D:G.37, D:S.39, D:S.40 Salt bridges: D:K.38, D:R.174

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.67, E.140 Ligands: PO4.1, UZR.4 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain B: S.39, E.140 Ligands: PO4.5 No protein-ligand interaction detected (PLIP) MG.13: 4 residues within 4Å: Chain C: D.67, E.140 Ligands: PO4.12, UZR.15 No protein-ligand interaction detected (PLIP) MG.17: 3 residues within 4Å: Chain D: S.39, E.140 Ligands: PO4.16 No protein-ligand interaction detected (PLIP)

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 1 residues within 4Å: Chain A: Q.58 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.58 GOL.7: 6 residues within 4Å: Chain A: E.199, L.203, P.204 Chain B: Y.146, R.151, Y.208 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.151, B:Y.208 GOL.8: 8 residues within 4Å: Chain B: P.91, N.96, I.99, L.143, A.144, Y.146, S.147, V.150 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.91, B:A.144 GOL.9: 1 residues within 4Å: Chain B: G.23 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.23, B:G.23 GOL.10: 5 residues within 4Å: Chain B: D.161, D.163 Chain D: L.203, K.206, K.207 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:D.163, B:A.164, D:L.203, D:K.206, D:K.207 GOL.14: 1 residues within 4Å: Chain C: Q.58 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.58 GOL.18: 6 residues within 4Å: Chain C: E.199, L.203, P.204 Chain D: Y.146, R.151, Y.208 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.151, D:Y.208 GOL.19: 8 residues within 4Å: Chain D: P.91, N.96, I.99, L.143, A.144, Y.146, S.147, V.150 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:P.91, D:A.144 GOL.20: 1 residues within 4Å: Chain D: G.23 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.23, D:G.23 GOL.21: 5 residues within 4Å: Chain B: L.203, K.206, K.207 Chain D: D.161, D.163 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:L.203, B:K.206, B:K.207, D:D.163, D:A.164

4 x UZR: 2'-deoxy-2'-triaza-1,2-dien-2-ium-1-yl-uridine-5'-monophosphate(Non-covalent)

UZR.4: 17 residues within 4Å: Chain A: T.34, A.35, K.38, D.67, Y.70, F.88, D.89, F.119, H.122, E.140, I.142, R.171, R.174, R.181, V.194 Ligands: PO4.1, MG.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:T.34, A:T.34, A:A.35, A:D.89, A:E.140, A:R.171, A:R.171, A:R.174 Water bridges: A:D.89, A:D.89 Salt bridges: A:K.38 UZR.11: 11 residues within 4Å: Chain B: T.34, K.38, D.67, Y.70, F.88, D.89, H.122, I.142, R.171, R.174 Ligands: PO4.5 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.88 Hydrogen bonds: B:T.34, B:Y.70, B:D.89, B:R.171, B:R.171, B:R.174 Water bridges: B:K.38, B:D.67 Salt bridges: B:K.38, B:R.171 UZR.15: 17 residues within 4Å: Chain C: T.34, A.35, K.38, D.67, Y.70, F.88, D.89, F.119, H.122, E.140, I.142, R.171, R.174, R.181, V.194 Ligands: PO4.12, MG.13 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:T.34, C:T.34, C:A.35, C:D.89, C:E.140, C:R.171, C:R.171, C:R.174 Water bridges: C:D.89, C:D.89 Salt bridges: C:K.38 UZR.22: 11 residues within 4Å: Chain D: T.34, K.38, D.67, Y.70, F.88, D.89, H.122, I.142, R.171, R.174 Ligands: PO4.16 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:F.88 Hydrogen bonds: D:T.34, D:Y.70, D:D.89, D:R.171, D:R.171, D:R.174 Water bridges: D:K.38, D:D.67 Salt bridges: D:K.38, 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
A

B
B

C
A

D
B

Uridine-cytidine kinase 2

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