SMTL ID : 2af6.5 (9 other biounits)

Crystal structure of Mycobacterium tuberculosis Flavin dependent thymidylate synthase (Mtb ThyX) in the presence of co-factor FAD and substrate analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (BrdUMP)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-dimer

Ligands

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 9 residues within 4Å: Chain A: R.95, H.96, R.97, H.98, H.194, M.198, R.199, H.203 Ligands: BRU.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:H.203 Hydrogen bonds: A:R.95, A:R.95, A:R.97, A:R.97, A:H.194, A:R.199 Water bridges: A:R.95, A:R.97, A:H.98, A:H.98, A:H.194 Salt bridges: A:H.96, A:H.96, A:R.97, A:R.97, A:H.194, A:H.194 FAD.7: 9 residues within 4Å: Chain B: R.95, H.96, R.97, H.98, H.194, M.198, R.199, H.203 Ligands: BRU.8 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:R.95, B:R.95, B:R.97, B:R.97, B:H.194, B:R.199 Water bridges: B:R.95, B:R.97, B:H.98, B:H.98 Salt bridges: B:H.96, B:H.96, B:R.97, B:R.97, B:H.194, B:H.194

2 x BRU: 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE(Non-covalent)

BRU.2: 5 residues within 4Å: Chain A: H.91, E.92, R.95, R.199 Ligands: FAD.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:R.95 Hydrogen bonds: A:H.91, A:E.92, A:R.95, A:R.199, A:R.199 Water bridges: A:E.92 BRU.8: 5 residues within 4Å: Chain B: H.91, E.92, R.95, R.199 Ligands: FAD.7 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:E.92, B:R.95 Hydrogen bonds: B:H.91, B:E.92, B:R.95, B:R.199, B:R.199 Water bridges: B:E.92, B:D.205

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 9 residues within 4Å: Chain A: K.14, T.15, G.31, G.32, A.76, S.77, V.78, Y.189, V.222 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.15, A:T.15, A:G.32, A:S.77, A:S.77 GOL.4: 6 residues within 4Å: Chain A: L.216, R.217, A.220, F.227, F.230, V.232 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.216, A:F.230 GOL.9: 6 residues within 4Å: Chain B: R.41, S.46, P.50, N.51, T.54, Y.60 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.41, B:R.41, B:S.46, B:N.51, B:T.54, B:H.63 Water bridges: B:S.46 GOL.10: 4 residues within 4Å: Chain B: H.69, S.71, V.72 Ligands: IOD.5 No protein-ligand interaction detected (PLIP)

2 x IOD: IODIDE ION(Non-functional Binders)

IOD.5: 5 residues within 4Å: Chain B: G.68, F.70, S.71, R.190 Ligands: GOL.10 Ligand excluded by PLIP IOD.6: 3 residues within 4Å: Chain B: K.14, Y.189, V.222 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sampathkumar, P. et al., Structure of the Mycobacterium tuberculosis Flavin Dependent Thymidylate Synthase (MtbThyX) at 2.0A Resolution. J.Mol.Biol. (2005)

Release Date

2005-10-04

Peptides

Thymidylate synthase thyX: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

Thymidylate synthase thyX

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