SMTL ID : 2af6.10 (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

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

IOD.1: 3 residues within 4Å: Chain A: R.193, H.194, A.247 Ligand excluded by PLIP IOD.2: 1 residues within 4Å: Chain A: T.4 Ligand excluded by PLIP IOD.8: 5 residues within 4Å: Chain B: G.68, F.70, S.71, R.190 Ligands: GOL.13 Ligand excluded by PLIP IOD.9: 3 residues within 4Å: Chain B: K.14, Y.189, V.222 Ligand excluded by PLIP

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

FAD.3: 15 residues within 4Å: Chain A: R.95, H.96, R.97, H.98, H.194, M.198, R.199, H.203 Chain B: S.100, S.102, Q.103, S.105, R.107, Y.108 Ligands: BRU.4 20 PLIP interactions: 17 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:H.203 Hydrogen bonds: A:R.95, A:R.95, A:R.97, A:R.97, A:H.98, A:H.194, A:R.199, B:S.100, B:Q.103, B:Q.103 Water bridges: A:H.96, 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.10: 14 residues within 4Å: Chain A: S.100, S.102, Q.103, S.105, R.107 Chain B: R.95, H.96, R.97, H.98, H.194, M.198, R.199, H.203 Ligands: BRU.11 20 PLIP interactions: 16 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.95, B:R.95, B:R.97, B:R.97, B:H.194, B:R.199, A:Q.103, A:Q.103 Water bridges: B:R.95, B:R.97, B:H.98, B:H.98, A:R.97, A:S.100 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.4: 13 residues within 4Å: Chain A: H.91, E.92, R.95, R.199 Chain B: R.87, Q.103, L.104, S.105, Q.106, R.107, Y.108, R.172 Ligands: FAD.3 16 PLIP interactions: 9 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:E.92, A:R.95 Hydrogen bonds: A:H.91, A:E.92, A:E.92, A:R.95, A:R.199, A:R.199, B:Q.106, B:R.107, B:R.107 Water bridges: A:D.205, B:R.87, B:R.172 Salt bridges: B:R.87, B:R.172 BRU.11: 12 residues within 4Å: Chain A: R.87, Q.103, L.104, S.105, Q.106, R.107, R.172 Chain B: H.91, E.92, R.95, R.199 Ligands: FAD.10 15 PLIP interactions: 8 interactions with chain B, 7 interactions with chain A 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, A:Q.106, A:R.107, A:R.107 Water bridges: B:D.205, A:R.87, A:R.87 Salt bridges: A:R.87, A:R.172

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 10 residues within 4Å: Chain A: K.14, T.15, G.31, G.32, P.33, 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:V.222 GOL.6: 5 residues within 4Å: Chain A: R.41, S.48, P.50, T.54, Y.60 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.41, A:R.41, A:T.54 Water bridges: A:S.46 GOL.7: 4 residues within 4Å: Chain A: G.68, H.69, S.71, V.72 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.68 Water bridges: A:S.71, A:S.71 GOL.12: 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.13: 4 residues within 4Å: Chain B: H.69, S.71, V.72 Ligands: IOD.8 No protein-ligand interaction detected (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
A

B
D

Thymidylate synthase thyX

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