SMTL ID : 4rzu.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 15 residues within 4Å: Chain A: I.12, D.13, G.14, S.15, G.16, K.17, S.18, S.19, R.138, G.190, K.192, T.193, P.194, I.197 Ligands: MG.3 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.14, A:S.15, A:G.16, A:K.17, A:S.18, A:S.19, A:S.19, A:R.138, A:K.192 Water bridges: A:K.17, A:K.17 Salt bridges: A:K.17 pi-Cation interactions: A:R.138 ADP.4: 12 residues within 4Å: Chain B: D.13, G.14, S.15, G.16, K.17, S.18, S.19, R.138, S.142, K.192, P.194 Ligands: MG.7 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.14, B:S.15, B:G.16, B:K.17, B:S.18, B:S.18, B:S.19, B:K.192 Salt bridges: B:K.17 pi-Cation interactions: B:R.138

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

EDO.2: 4 residues within 4Å: Chain A: D.108, W.111 Chain B: S.117, F.118 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.117, A:D.108 EDO.5: 4 residues within 4Å: Chain B: F.63, R.105, D.154 Ligands: PGE.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.154

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: S.18, D.92 Ligands: ADP.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.18, H2O.1, H2O.1 MG.7: 2 residues within 4Å: Chain B: S.18 Ligands: ADP.4 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.18, H2O.1

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

PGE.6: 6 residues within 4Å: Chain B: H.46, H.67, P.148, A.153, D.154 Ligands: EDO.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Biswas, A. et al., Crystal structure of ADP bound dTMP kinase (st1543) from Sulfolobus Tokodaii Strain7. To be Published

Release Date

2015-12-30

Peptides

Probable thymidylate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Probable thymidylate kinase

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