SMTL ID : 2orw.1

Thermotoga maritima thymidine kinase 1 like enzyme in complex with TP4A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.140, C.143, C.173, C.176 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.140, A:C.143, A:C.173, A:C.176 ZN.3: 4 residues within 4Å: Chain B: C.140, C.143, C.173, C.176 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.140, B:C.143, B:C.173, B:C.176 ZN.7: 4 residues within 4Å: Chain C: C.140, C.143, C.173, C.176 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.140, C:C.143, C:C.173, C:C.176 ZN.9: 4 residues within 4Å: Chain D: C.140, C.143, C.173, C.176 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.140, D:C.143, D:C.173, D:C.176

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.17, D.83 Ligands: 4TA.5 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.17, H2O.6, H2O.11, H2O.14 MG.4: 3 residues within 4Å: Chain B: T.17, D.83 Ligands: 4TA.6 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.17, H2O.8, H2O.14, H2O.14 MG.8: 3 residues within 4Å: Chain C: T.17, D.83 Ligands: 4TA.11 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.17, H2O.20, H2O.25, H2O.28 MG.10: 3 residues within 4Å: Chain D: T.17, D.83 Ligands: 4TA.12 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:T.17, H2O.22, H2O.28, H2O.29

4 x 4TA: P1-(5'-ADENOSYL)P4-(5'-(2'-DEOXY-THYMIDYL))TETRAPHOSPHATE(Non-covalent)

4TA.5: 27 residues within 4Å: Chain A: P.11, M.12, Y.13, S.14, G.15, K.16, T.17, T.18, S.52, E.84, Q.86, F.87, L.111, T.114, H.115, A.138, V.139, T.151, E.160, I.161, D.162, V.163, G.164, Y.169 Chain D: E.25, L.29 Ligands: MG.2 28 PLIP interactions: 27 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:L.111, A:T.151, A:Y.169, A:Y.169 Hydrogen bonds: A:Y.13, A:S.14, A:G.15, A:K.16, A:T.17, A:T.17, A:T.18, A:Q.86, A:H.115, A:H.115, A:V.139, A:V.139, A:E.160, A:D.162, A:G.164, A:G.164, A:Y.169, D:E.25 Water bridges: A:Y.13, A:L.111, A:A.171 Salt bridges: A:K.16, A:K.16, A:K.16 4TA.6: 28 residues within 4Å: Chain B: P.11, M.12, Y.13, S.14, G.15, K.16, T.17, T.18, S.52, E.84, Q.86, F.87, L.111, T.114, H.115, F.120, A.138, V.139, T.151, E.160, I.161, D.162, V.163, G.164, Y.169 Chain C: E.25, L.29 Ligands: MG.4 30 PLIP interactions: 29 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.111, B:T.151, B:Y.169, B:Y.169 Hydrogen bonds: B:Y.13, B:S.14, B:G.15, B:K.16, B:T.17, B:T.17, B:T.18, B:Q.86, B:H.115, B:V.139, B:V.139, B:E.160, B:D.162, B:G.164, B:G.164, B:Y.169, C:E.25 Water bridges: B:T.17, B:T.18, B:D.83, B:L.111, B:A.171 Salt bridges: B:K.16, B:K.16, B:K.16 pi-Stacking: B:Y.169 4TA.11: 27 residues within 4Å: Chain B: E.25, L.29 Chain C: P.11, M.12, Y.13, S.14, G.15, K.16, T.17, T.18, S.52, E.84, Q.86, F.87, L.111, T.114, H.115, A.138, V.139, T.151, E.160, I.161, D.162, V.163, G.164, Y.169 Ligands: MG.8 28 PLIP interactions: 26 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:L.111, C:T.151, C:Y.169, C:Y.169 Hydrogen bonds: C:Y.13, C:S.14, C:G.15, C:K.16, C:T.17, C:T.17, C:T.18, C:T.18, C:Q.86, C:H.115, C:V.139, C:V.139, C:E.160, C:D.162, C:G.164, C:G.164, C:Y.169, B:E.25 Water bridges: C:L.111, C:A.171, B:E.25 Salt bridges: C:K.16, C:K.16, C:K.16 4TA.12: 28 residues within 4Å: Chain A: E.25, L.29 Chain D: P.11, M.12, Y.13, S.14, G.15, K.16, T.17, T.18, S.52, E.84, Q.86, F.87, L.111, T.114, H.115, F.120, A.138, V.139, T.151, E.160, I.161, D.162, V.163, G.164, Y.169 Ligands: MG.10 32 PLIP interactions: 3 interactions with chain A, 29 interactions with chain D Hydrogen bonds: A:E.25, D:Y.13, D:S.14, D:G.15, D:K.16, D:T.17, D:T.17, D:T.18, D:T.18, D:Q.86, D:H.115, D:V.139, D:V.139, D:E.160, D:D.162, D:G.164, D:G.164, D:Y.169 Water bridges: A:E.25, A:E.25, D:T.17, D:D.83, D:L.111, D:A.171 Hydrophobic interactions: D:L.111, D:T.151, D:Y.169, D:Y.169 Salt bridges: D:K.16, D:K.16, D:K.16 pi-Stacking: D:Y.169

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Segura-Pena, D. et al., Binding of ATP to TK1-like Enzymes Is Associated with a Conformational Change in the Quaternary Structure. J.Mol.Biol. (2007)

Release Date

2007-03-27

Peptides

Thymidine kinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Thymidine kinase

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