SMTL ID : 1gsi.1

CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE (TMP)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 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: TMP.2 6 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: A:D.9, A:E.166, TMP.2, H2O.8, H2O.8, H2O.10 MG.9: 3 residues within 4Å: Chain B: D.9, E.166 Ligands: TMP.10 6 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: B:D.9, B:E.166, TMP.10, H2O.18, H2O.19, H2O.21

2 x TMP: THYMIDINE-5'-PHOSPHATE(Non-covalent)

TMP.2: 12 residues within 4Å: Chain A: D.9, F.36, P.37, Y.39, F.70, R.74, R.95, S.99, N.100, Y.103, Y.165 Ligands: MG.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.36, A:P.37, A:Y.103 Hydrogen bonds: A:R.74, A:R.74, A:N.100 Water bridges: A:K.13, A:F.36, A:D.94, A:R.95, A:R.95, A:D.163, A:D.163 Salt bridges: A:R.95 pi-Stacking: A:F.70 TMP.10: 12 residues within 4Å: Chain B: D.9, F.36, P.37, Y.39, F.70, R.74, R.95, S.99, N.100, Y.103, Y.165 Ligands: MG.9 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:F.36, B:P.37, B:Y.103 Hydrogen bonds: B:Y.39, B:R.74, B:R.74, B:N.100 Water bridges: B:K.13, B:F.36, B:D.94, B:R.95, B:R.95, B:D.163, B:D.163 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 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:G.10, A:A.11, A:G.12, A:K.13, A:R.14 Water bridges: A:G.12, A:K.13, A:K.13, A:K.13, A:T.15, A:R.153, A:R.153, A:R.153 Salt bridges: A:K.13, A:R.153 SO4.4: 5 residues within 4Å: Chain A: A.154, Q.155, 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 SO4.5: 6 residues within 4Å: Chain A: W.119, R.122, I.123, R.127 Chain B: E.55, H.56 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:R.127 Salt bridges: A:R.122, B:H.56 Water bridges: B:E.50, B:E.55, B:H.56 SO4.11: 7 residues within 4Å: Chain B: V.8, G.10, A.11, G.12, K.13, R.14, R.153 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:G.10, B:A.11, B:G.12, B:K.13, B:R.14 Water bridges: B:G.12, B:K.13, B:K.13, B:K.13, B:T.15, B:R.153, B:R.153, B:R.153 Salt bridges: B:K.13, B:R.153 SO4.12: 5 residues within 4Å: Chain B: A.154, Q.155, 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 SO4.13: 6 residues within 4Å: Chain A: E.55, H.56 Chain B: W.119, R.122, I.123, R.127 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Water bridges: A:E.50, A:E.55 Salt bridges: A:H.56, B:R.122 Hydrogen bonds: B:R.127

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

ACT.6: 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.7: 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.8: 2 residues within 4Å: Chain A: Y.39, H.53 No protein-ligand interaction detected (PLIP) ACT.14: 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.15: 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 ACT.16: 2 residues within 4Å: Chain B: Y.39, H.53 No protein-ligand interaction detected (PLIP)

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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