SMTL ID : 1gtv.1 (1 other biounit)

CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE-5'-DIPHOSPHATE (TDP)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.9, E.166 Ligands: TYD.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.9, A:E.166, H2O.193, H2O.244 MG.9: 3 residues within 4Å: Chain B: D.9, E.166 Ligands: TYD.10 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.9, B:E.166, H2O.443, H2O.494

2 x TYD: THYMIDINE-5'-DIPHOSPHATE(Non-covalent)

TYD.2: 16 residues within 4Å: Chain A: D.9, F.36, P.37, Y.39, L.52, F.70, R.74, R.95, S.99, N.100, Y.103, D.163, Y.165, E.166 Ligands: MG.1, ACT.5 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:P.37, A:Y.103 Hydrogen bonds: A:Y.39, A:R.74, A:R.74, A:N.100, A:E.166 Water bridges: A:D.9, A:D.9 Salt bridges: A:R.95 pi-Stacking: A:F.70 TYD.10: 16 residues within 4Å: Chain B: D.9, F.36, P.37, Y.39, L.52, F.70, R.74, R.95, S.99, N.100, Y.103, D.163, Y.165, E.166 Ligands: MG.9, ACT.13 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:P.37, B:Y.103 Hydrogen bonds: B:Y.39, B:Y.39, B:R.74, B:R.74, B:N.100, B:D.163 Water bridges: B:D.9, B:D.9, B:D.9, B:D.9 Salt bridges: B:R.95 pi-Stacking: B:F.70

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 7 residues within 4Å: Chain A: V.8, G.10, A.11, G.12, K.13, R.14, R.153 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.10, A:A.11, A:G.12, A:K.13, A:R.14 Salt bridges: A:K.13, A:R.153 SO4.4: 4 residues within 4Å: Chain A: A.154, A.161, R.162, R.167 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.162 Salt bridges: A:R.162, A:R.167 SO4.6: 6 residues within 4Å: Chain A: W.119, R.122, I.123, R.127 Chain B: E.55, H.56 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Water bridges: B:E.55, A:R.122 Salt bridges: B:H.56, A:R.122 Hydrogen bonds: A:R.127 SO4.11: 7 residues within 4Å: Chain B: V.8, G.10, A.11, G.12, K.13, R.14, R.153 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.10, B:A.11, B:G.12, B:K.13, B:R.14 Salt bridges: B:K.13, B:R.153 SO4.12: 4 residues within 4Å: Chain B: A.154, A.161, R.162, R.167 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.162 Salt bridges: B:R.162, B:R.167 SO4.14: 6 residues within 4Å: Chain A: E.55, H.56 Chain B: W.119, R.122, I.123, R.127 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.127 Water bridges: B:R.122 Salt bridges: B:R.122, A:H.56

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 4 residues within 4Å: Chain A: Y.39, A.49, H.53 Ligands: TYD.2 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.53 ACT.7: 3 residues within 4Å: Chain A: V.43, D.46 Chain B: R.127 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.43 Hydrogen bonds: A:D.46 Salt bridges: B:R.127 ACT.8: 4 residues within 4Å: Chain A: R.25, S.30, V.31, Y.88 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.31 Salt bridges: A:R.25 ACT.13: 4 residues within 4Å: Chain B: Y.39, A.49, H.53 Ligands: TYD.10 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.53 ACT.15: 3 residues within 4Å: Chain A: R.127 Chain B: V.43, D.46 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.43 Hydrogen bonds: B:D.46, B:D.46 Salt bridges: A:R.127 ACT.16: 4 residues within 4Å: Chain B: R.25, S.30, V.31, Y.88 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.31 Salt bridges: B:R.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ursby, T. et al., Cryophotolysis of Caged Compounds: A Technique for Trapping Intermediate States in Protein Crystals. Acta Crystallogr.,Sect.D (2002)

Release Date

2002-03-28

Peptides

THYMIDYLATE KINASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

THYMIDYLATE KINASE

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