SMTL ID : 2b8t.1

Crystal structure of Thymidine Kinase from U.urealyticum in complex with thymidine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.153, C.156, C.191, H.194 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.153, A:C.156, A:C.191, A:H.194 ZN.3: 4 residues within 4Å: Chain B: C.153, C.156, C.191, H.194 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.153, B:C.156, B:C.191, B:H.194 ZN.5: 4 residues within 4Å: Chain C: C.153, C.156, C.191, H.194 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.153, C:C.156, C:C.191, C:H.194 ZN.7: 4 residues within 4Å: Chain D: C.153, C.156, C.191, H.194 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.153, D:C.156, D:C.191, D:H.194

4 x THM: THYMIDINE(Non-covalent)

THM.2: 16 residues within 4Å: Chain A: M.21, E.97, F.100, L.124, K.126, N.127, F.128, F.133, S.163, R.165, I.178, V.179, K.180, I.181, G.182, Y.187 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.124, A:F.133, A:Y.187, A:Y.187 Hydrogen bonds: A:F.128, A:R.165, A:I.178, A:K.180, A:G.182, A:Y.187 THM.4: 15 residues within 4Å: Chain B: M.21, E.97, F.100, L.124, N.127, F.128, F.133, S.163, R.165, I.178, V.179, K.180, I.181, G.182, Y.187 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.124, B:Y.187, B:Y.187 Hydrogen bonds: B:F.128, B:R.165, B:I.178, B:K.180, B:G.182, B:Y.187 pi-Stacking: B:F.133 THM.6: 16 residues within 4Å: Chain C: M.21, E.97, F.100, L.124, K.126, N.127, F.128, F.133, S.163, R.165, I.178, V.179, K.180, I.181, G.182, Y.187 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:F.133, C:Y.187, C:Y.187 Hydrogen bonds: C:Q.99, C:F.128, C:R.165, C:I.178, C:K.180, C:G.182, C:Y.187 THM.8: 16 residues within 4Å: Chain D: M.21, E.97, Q.99, F.100, L.124, N.127, F.128, F.133, S.163, R.165, I.178, V.179, K.180, I.181, G.182, Y.187 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:L.124, D:F.133, D:Y.187, D:Y.187 Hydrogen bonds: D:Q.99, D:F.128, D:R.165, D:I.178, D:K.180, D:Y.187

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.9: 8 residues within 4Å: Chain D: P.20, M.21, F.22, A.23, G.24, K.25, T.26, R.61 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:P.20, D:F.22, D:A.23, D:G.24, D:K.25, D:K.25, D:T.26, D:T.26, D:R.61 Water bridges: D:T.26, D:T.26, D:R.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kosinska, U. et al., Structure of the substrate complex of thymidine kinase from Ureaplasma urealyticum and investigations of possible drug targets for the enzyme. FEBS Lett. (2005)

Release Date

2005-12-20

Peptides

Thymidine kinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Thymidine kinase