SMTL ID : 2qq0.1

Thymidine Kinase from Thermotoga Maritima in complex with thymidine + AppNHp

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.5: 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.9: 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.13: 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: 2 residues within 4Å: Chain A: T.17 Ligands: ANP.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.17, H2O.1, H2O.1, H2O.6 MG.6: 4 residues within 4Å: Chain B: T.17, D.83 Ligands: TMP.7, ADP.8 5 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: B:T.17, TMP.7, H2O.9, H2O.12, H2O.13 MG.10: 2 residues within 4Å: Chain C: T.17 Ligands: ANP.12 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.17, H2O.16, H2O.16, H2O.21 MG.14: 4 residues within 4Å: Chain D: T.17, D.83 Ligands: TMP.15, ADP.16 5 PLIP interactions: 1 interactions with chain D, 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: D:T.17, TMP.15, H2O.24, H2O.26, H2O.28

2 x THM: THYMIDINE(Non-covalent)

THM.3: 16 residues within 4Å: Chain A: M.12, E.84, Q.86, F.87, L.111, T.114, H.115, F.120, T.151, E.160, I.161, D.162, V.163, G.164, Y.169 Ligands: ANP.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.111, A:T.151, A:Y.169, A:Y.169 Hydrogen bonds: A:Q.86, A:H.115, A:E.160, A:D.162, A:G.164, A:Y.169 Water bridges: A:K.16, A:E.84 THM.11: 16 residues within 4Å: Chain C: M.12, E.84, Q.86, F.87, L.111, T.114, H.115, F.120, T.151, E.160, I.161, D.162, V.163, G.164, Y.169 Ligands: ANP.12 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:L.111, C:T.151, C:Y.169, C:Y.169 Hydrogen bonds: C:Q.86, C:H.115, C:E.160, C:D.162, C:G.164, C:Y.169 Water bridges: C:K.16, C:E.84

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.4: 19 residues within 4Å: Chain A: P.11, M.12, Y.13, S.14, G.15, K.16, T.17, T.18, S.52, H.53, E.84, L.111, A.138, V.139, Q.166 Chain D: E.25, L.29 Ligands: MG.2, THM.3 28 PLIP interactions: 24 interactions with chain A, 4 interactions with chain D Hydrogen bonds: A:Y.13, A:S.14, A:G.15, A:K.16, A:K.16, A:T.17, A:T.17, A:T.18, A:H.53, A:V.139, A:V.139, A:Q.166, D:E.25 Water bridges: A:T.17, A:T.18, A:T.18, A:T.18, A:T.18, A:V.51, A:H.53, A:H.53, A:E.84, A:G.164, A:A.171, D:E.25, D:E.25, D:E.25 Salt bridges: A:H.53 ANP.12: 19 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, H.53, E.84, L.111, A.138, V.139, Q.166 Ligands: MG.10, THM.11 25 PLIP interactions: 2 interactions with chain B, 23 interactions with chain C Hydrogen bonds: B:E.25, C:Y.13, C:S.14, C:G.15, C:K.16, C:K.16, C:T.17, C:T.18, C:T.18, C:H.53, C:V.139, C:V.139, C:Q.166 Water bridges: B:E.25, C:T.17, C:T.18, C:T.18, C:V.51, C:H.53, C:H.53, C:E.84, C:E.84, C:G.164, C:A.171 Salt bridges: C:H.53

2 x TMP: THYMIDINE-5'-PHOSPHATE(Non-covalent)

TMP.7: 20 residues within 4Å: Chain B: M.12, Y.13, K.16, H.53, E.84, Q.86, F.87, L.111, T.114, H.115, F.120, T.151, E.160, I.161, D.162, V.163, G.164, Y.169 Ligands: MG.6, ADP.8 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:L.111, B:T.151, B:Y.169, B:Y.169 Hydrogen bonds: B:Y.13, B:T.17, B:Q.86, B:H.115, B:H.115, B:E.160, B:D.162, B:G.164, B:Y.169 Water bridges: B:K.16, B:T.17, B:T.17, B:L.111 Salt bridges: B:K.16, B:H.53 pi-Stacking: B:Y.169 TMP.15: 20 residues within 4Å: Chain D: M.12, Y.13, K.16, H.53, E.84, Q.86, F.87, L.111, T.114, H.115, F.120, T.151, E.160, I.161, D.162, V.163, G.164, Y.169 Ligands: MG.14, ADP.16 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:L.111, D:T.151, D:Y.169, D:Y.169 Hydrogen bonds: D:Y.13, D:T.17, D:Q.86, D:H.115, D:E.160, D:D.162, D:G.164, D:Y.169 Water bridges: D:K.16, D:T.17, D:T.17, D:L.111 Salt bridges: D:K.16, D:H.53 pi-Stacking: D:Y.169

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.8: 15 residues within 4Å: Chain B: P.11, Y.13, S.14, G.15, K.16, T.17, T.18, S.52, H.53, A.138, V.139 Chain C: E.25, L.29 Ligands: MG.6, TMP.7 20 PLIP interactions: 18 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:Y.13, B:S.14, B:G.15, B:K.16, B:T.17, B:T.17, B:T.18, B:H.53, B:V.139, B:V.139, C:E.25 Water bridges: B:T.17, B:T.18, B:T.18, B:H.53, B:A.171, C:E.25 Salt bridges: B:K.16, B:H.53, B:H.53 ADP.16: 15 residues within 4Å: Chain A: E.25, L.29 Chain D: P.11, Y.13, S.14, G.15, K.16, T.17, T.18, S.52, H.53, A.138, V.139 Ligands: MG.14, TMP.15 21 PLIP interactions: 20 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:Y.13, D:S.14, D:G.15, D:K.16, D:T.17, D:T.18, D:T.18, D:H.53, D:V.139, D:V.139, A:E.25 Water bridges: D:T.17, D:T.17, D:T.17, D:T.18, D:V.51, D:D.83, D:A.171 Salt bridges: D:K.16, D:H.53, D:H.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Segura-Pena, D. et al., Quaternary structure change as a mechanism for the regulation of thymidine kinase 1-like enzymes. Structure (2007)

Release Date

2007-10-16

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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