SMTL ID : 6n54.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.42 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: E.140 Ligands: PO4.3, KEA.4 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain B: E.140 Ligands: PO4.12, KEA.13 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain C: E.140 Ligands: PO4.16, KEA.17 No protein-ligand interaction detected (PLIP) MG.18: 3 residues within 4Å: Chain D: E.140 Ligands: PO4.25, KEA.26 No protein-ligand interaction detected (PLIP)

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 2 residues within 4Å: Chain A: N.52, R.57 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.52, A:R.57 GOL.6: 4 residues within 4Å: Chain B: R.151, D.152, Y.208 Ligands: GOL.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.151, B:D.152 GOL.7: 7 residues within 4Å: Chain B: P.91, F.94, N.96, I.99, L.143, Y.146, S.147 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.91, B:S.147 Water bridges: B:L.143, B:S.147 GOL.8: 6 residues within 4Å: Chain A: E.199, L.203, P.204 Chain B: Y.146, R.151, Y.208 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.146, B:R.151, B:Y.208 GOL.9: 4 residues within 4Å: Chain B: K.157, Y.208 Chain D: R.215 Ligands: GOL.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.210 Water bridges: B:K.157 GOL.10: 4 residues within 4Å: Chain B: K.206, K.207 Chain D: D.161, D.163 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:T.162, B:K.206 Water bridges: D:T.162, B:K.207, B:K.207 GOL.11: 4 residues within 4Å: Chain B: V.62, I.63, L.64, V.131 2 PLIP interactions: 2 interactions with chain B Water bridges: B:S.68, B:S.68 GOL.15: 2 residues within 4Å: Chain C: N.52, R.57 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.52, C:R.57 GOL.19: 4 residues within 4Å: Chain D: R.151, D.152, Y.208 Ligands: GOL.22 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.151, D:D.152 GOL.20: 7 residues within 4Å: Chain D: P.91, F.94, N.96, I.99, L.143, Y.146, S.147 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:P.91, D:S.147 Water bridges: D:L.143, D:S.147 GOL.21: 6 residues within 4Å: Chain C: E.199, L.203, P.204 Chain D: Y.146, R.151, Y.208 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.146, D:R.151, D:Y.208 GOL.22: 4 residues within 4Å: Chain B: R.215 Chain D: K.157, Y.208 Ligands: GOL.19 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.210 Water bridges: D:K.157 GOL.23: 4 residues within 4Å: Chain B: D.161, D.163 Chain D: K.206, K.207 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:K.206, B:T.162 Water bridges: D:K.207, D:K.207, B:T.162 GOL.24: 4 residues within 4Å: Chain D: V.62, I.63, L.64, V.131 2 PLIP interactions: 2 interactions with chain D Water bridges: D:S.68, D:S.68

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

PO4.3: 9 residues within 4Å: Chain A: G.33, A.35, S.36, G.37, K.38, S.39, R.174 Ligands: MG.1, KEA.4 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.33, A:A.35, A:S.36, A:G.37, A:K.38, A:S.39 Water bridges: A:S.39, A:S.40 Salt bridges: A:K.38, A:R.174 PO4.12: 10 residues within 4Å: Chain B: G.33, A.35, S.36, G.37, K.38, S.39, E.140, R.174 Ligands: MG.5, KEA.13 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, B:S.39 Water bridges: B:S.39, B:S.40 Salt bridges: B:K.38, B:R.174 PO4.16: 9 residues within 4Å: Chain C: G.33, A.35, S.36, G.37, K.38, S.39, R.174 Ligands: MG.14, KEA.17 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:G.33, C:A.35, C:S.36, C:G.37, C:K.38, C:S.39 Water bridges: C:S.39, C:S.40 Salt bridges: C:K.38, C:R.174 PO4.25: 10 residues within 4Å: Chain D: G.33, A.35, S.36, G.37, K.38, S.39, E.140, R.174 Ligands: MG.18, KEA.26 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, D:S.39 Water bridges: D:S.39, D:S.40 Salt bridges: D:K.38, D:R.174

4 x KEA: 2'-azido-2'-deoxycytidine 5'-(dihydrogen phosphate)(Non-covalent)

KEA.4: 14 residues within 4Å: Chain A: T.34, A.35, K.38, D.67, Y.70, F.88, D.89, F.119, H.122, I.142, R.171, R.174 Ligands: MG.1, PO4.3 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.70, A:F.88 Hydrogen bonds: A:T.34, A:T.34, A:A.35, A:Y.117, A:H.122, A:R.171, A:R.171, A:R.174 Water bridges: A:D.89, A:I.142 Salt bridges: A:K.38 pi-Stacking: A:F.119 KEA.13: 15 residues within 4Å: Chain B: T.34, A.35, K.38, D.67, Y.70, F.88, D.89, F.119, H.122, I.142, R.171, R.174, V.194 Ligands: MG.5, PO4.12 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.88, B:F.119 Hydrogen bonds: B:T.34, B:A.35, B:D.67, B:Y.70, B:H.122, B:R.171, B:R.171, B:R.174 Salt bridges: B:K.38, B:R.171 KEA.17: 14 residues within 4Å: Chain C: T.34, A.35, K.38, D.67, Y.70, F.88, D.89, F.119, H.122, I.142, R.171, R.174 Ligands: MG.14, PO4.16 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:Y.70, C:F.88 Hydrogen bonds: C:T.34, C:T.34, C:A.35, C:Y.117, C:H.122, C:R.171, C:R.171, C:R.174 Water bridges: C:D.89, C:I.142 Salt bridges: C:K.38 pi-Stacking: C:F.119 KEA.26: 15 residues within 4Å: Chain D: T.34, A.35, K.38, D.67, Y.70, F.88, D.89, F.119, H.122, I.142, R.171, R.174, V.194 Ligands: MG.18, PO4.25 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:F.88, D:F.119 Hydrogen bonds: D:T.34, D:A.35, D:D.67, D:Y.70, D:H.122, D:R.171, D:R.171, D:R.174 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

Related Entries With Identical Sequence