SMTL ID : 4nzy.1

Crystal structure (type-2) of dTMP kinase (st1543) from Sulfolobus Tokodaii Strain7

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.1: 7 residues within 4Å: Chain A: Y.35, T.37, S.41, S.42, D.43, R.74, Y.78 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.35, A:T.37, A:R.74 Salt bridges: A:D.43, A:D.43, A:R.74

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

PO4.2: 7 residues within 4Å: Chain A: I.12, D.13, G.14, S.15, G.16, K.17, S.18 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.14, A:G.14, A:G.16, A:S.18, A:S.18 Water bridges: A:D.13 Salt bridges: A:K.17 PO4.14: 7 residues within 4Å: Chain B: I.12, D.13, G.14, S.15, G.16, K.17, S.18 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.14, B:S.15, B:G.16, B:S.18, B:S.18, B:S.18 Salt bridges: B:K.17

8 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 5 residues within 4Å: Chain A: V.107, D.108, W.111 Chain B: S.117, F.118 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.108 PEG.4: 8 residues within 4Å: Chain A: W.39, N.40, S.42, H.67, D.70, F.71, R.74, R.101 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.70, A:R.74, A:R.74 Water bridges: A:K.50, A:H.67, A:H.67, A:R.101 PEG.5: 3 residues within 4Å: Chain A: K.195, I.199, R.202 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.195 PEG.6: 5 residues within 4Å: Chain A: S.103, L.171, E.174, V.175, K.178 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.178 PEG.7: 9 residues within 4Å: Chain A: Y.96, P.122, D.123, I.124, T.125, E.183, N.184, F.185 Ligands: PG4.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.96, A:T.125, A:T.125, A:T.125 PEG.15: 6 residues within 4Å: Chain A: S.117, F.118 Chain B: V.107, D.108, W.111 Ligands: 1PE.22 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.117, B:D.108 PEG.16: 3 residues within 4Å: Chain B: K.53, K.54, D.56 No protein-ligand interaction detected (PLIP) PEG.17: 6 residues within 4Å: Chain B: R.129, S.131, P.132, G.170, T.173, E.174 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.129, B:R.129

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 3 residues within 4Å: Chain A: R.129, V.130, D.189 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.129, A:T.191 EDO.9: 3 residues within 4Å: Chain A: R.129, D.177, V.187 No protein-ligand interaction detected (PLIP) EDO.10: 4 residues within 4Å: Chain A: R.93, R.101, Q.149, Y.168 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.101 Water bridges: A:D.13, A:R.105, A:Q.169 EDO.11: 3 residues within 4Å: Chain A: Q.200, K.203, F.204 No protein-ligand interaction detected (PLIP) EDO.18: 3 residues within 4Å: Chain B: L.58, F.63, D.154 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.154 EDO.19: 4 residues within 4Å: Chain B: S.117, F.118, A.119, I.120 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.119 Water bridges: B:K.121 EDO.20: 2 residues within 4Å: Chain B: K.53, L.57 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.56, B:D.56 EDO.21: 6 residues within 4Å: Chain B: H.67, F.71, Y.94, A.98, R.101, Y.116 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.67, B:R.101, B:R.101

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.12: 5 residues within 4Å: Chain A: K.121, D.123, E.183, N.184 Ligands: PEG.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.121

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.13: 4 residues within 4Å: Chain B: S.103, E.174, V.175, K.178 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.178

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.22: 6 residues within 4Å: Chain A: K.114, S.117 Chain B: D.110, W.111, K.114 Ligands: PEG.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.114, A:S.117 Water bridges: A:K.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Biswas, A. et al., Insight into Substrate Binding Mechanism in Thymidylate Kinase based on Intrinsic Dynamics of the Active Site. To be Published

Release Date

2014-12-24

Peptides

Probable thymidylate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Probable thymidylate kinase

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