SMTL ID : 2plr.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 6 residues within 4Å: Chain A: I.12, D.13, R.93, Q.169, I.172 Ligands: CL.2 Ligand excluded by PLIP CL.2: 3 residues within 4Å: Chain A: R.101, Y.168 Ligands: CL.1 Ligand excluded by PLIP

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

PO4.3: 8 residues within 4Å: Chain A: I.12, D.13, G.14, S.15, G.16, K.17, S.18 Ligands: PEG.15 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.14, A:G.14, A:G.16, A:S.18, A:S.18, A:S.18, A:S.18 Water bridges: A:K.17, A:K.17, A:S.19 Salt bridges: A:K.17

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

1PE.4: 7 residues within 4Å: Chain A: K.114, S.117 Chain B: D.110, W.111, K.114 Ligands: 1PE.21, PEG.26 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.114, A:S.117 Water bridges: A:K.113 1PE.20: 5 residues within 4Å: Chain B: S.103, I.109, E.174, V.175, K.178 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.178 1PE.21: 4 residues within 4Å: Chain B: D.110, K.113, K.114 Ligands: 1PE.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.110, B:K.114, B:K.114

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

PGE.5: 6 residues within 4Å: Chain A: S.103, I.109, L.171, E.174, V.175, K.178 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.174, A:K.178 PGE.6: 3 residues within 4Å: Chain A: R.129, D.177 Ligands: PEG.17 No protein-ligand interaction detected (PLIP) PGE.7: 4 residues within 4Å: Chain A: Q.200, K.203, F.204, E.207 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.203, A:E.207

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

EDO.8: 3 residues within 4Å: Chain A: E.29, K.31, R.32 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.31 Water bridges: A:R.32 EDO.9: 3 residues within 4Å: Chain A: R.77, Y.78, M.82 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.78 EDO.10: 3 residues within 4Å: Chain A: W.27, L.30, K.31 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.31 EDO.22: 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.23: 1 residues within 4Å: Chain B: K.55 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.55 EDO.24: 2 residues within 4Å: Chain B: I.186, F.204 No protein-ligand interaction detected (PLIP)

1 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.11: 9 residues within 4Å: Chain A: P.60, F.63, S.64, H.67, R.101, D.102, R.105, D.154 Ligands: PEG.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.64 Water bridges: A:H.67

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

EPE.12: 7 residues within 4Å: Chain A: Y.35, T.37, S.41, S.42, D.43, R.74, Y.78 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Water bridges: B:K.55, B:K.55, A:Y.78 Salt bridges: A:D.43, A:D.43, A:R.74

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

PEG.13: 7 residues within 4Å: Chain A: W.39, N.40, S.42, H.67, D.70, F.71, R.74 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.70, A:R.74, A:R.101 Water bridges: A:K.50 PEG.14: 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.15: 4 residues within 4Å: Chain A: G.14, G.16, R.138 Ligands: PO4.3 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.144 PEG.16: 4 residues within 4Å: Chain A: L.23, K.195, I.199, R.202 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.195 Water bridges: A:R.202 PEG.17: 5 residues within 4Å: Chain A: R.129, D.177, V.180, V.187 Ligands: PGE.6 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.129, A:D.177 PEG.18: 3 residues within 4Å: Chain A: F.63, D.154 Ligands: DTT.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.154 Water bridges: A:A.153 PEG.19: 2 residues within 4Å: Chain A: N.184, I.186 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.184, A:F.185 PEG.26: 6 residues within 4Å: Chain A: S.117, F.118 Chain B: V.107, D.108, W.111 Ligands: 1PE.4 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.108 PEG.27: 3 residues within 4Å: Chain B: K.53, K.54, D.56 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.54 PEG.28: 3 residues within 4Å: Chain B: L.58, F.63, D.154 No protein-ligand interaction detected (PLIP) PEG.29: 6 residues within 4Å: Chain B: L.136, K.140, S.160, E.162, E.163, L.166 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.140

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

PG4.25: 4 residues within 4Å: Chain B: R.129, D.177, V.180, V.187 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.129, B:R.129, B:D.177 Water bridges: B:G.190

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kanaujia, S.P. et al., Crystal structure of dTMP kinase (st1543) from Sulfolobus Tokodaii Strain7. To be Published

Release Date

2008-04-22

Peptides

Probable thymidylate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Probable thymidylate kinase

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