SMTL ID : 5h70.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 16 residues within 4Å: Chain A: I.12, D.13, G.14, S.15, G.16, K.17, S.18, S.19, R.138, S.142, G.190, K.192, T.193, P.194, I.197 Ligands: MG.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:I.12, A:G.14, A:S.15, A:G.16, A:G.16, A:K.17, A:S.18, A:S.19, A:S.19, A:K.192 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 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.14, B:S.15, B:G.16, B:G.16, B:K.17, B:S.18, B:S.19, 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: V.107, D.108, W.111 Chain B: F.118 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.108 EDO.5: 4 residues within 4Å: Chain B: F.63, R.105, D.154 Ligands: PGE.6 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: K.17, 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: 4 residues within 4Å: Chain B: K.17, S.18, D.92 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, Q.149, D.154 Ligands: EDO.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.46, 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

2016-12-07

Peptides

Probable thymidylate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Probable thymidylate kinase

Related Entries With Identical Sequence