SMTL ID : 5uin.1

X-ray structure of the W305A variant of the FdtF N-formyltransferase from salmonella enteric O60

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

TYD.1: 10 residues within 4Å: Chain A: K.15, E.82, Y.112, T.113, S.114, Y.159, Y.202, F.225, Y.228, Q.229 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:E.82, A:S.114, A:Y.228, A:Q.229, A:Q.229 Water bridges: A:K.15, A:K.15, A:K.15, A:T.113, A:S.114, A:Y.202, A:Y.228 Salt bridges: A:K.15, A:K.15 pi-Stacking: A:Y.202, A:Y.228 TYD.8: 11 residues within 4Å: Chain B: K.15, Q.50, E.82, Y.112, T.113, S.114, Y.159, Y.202, F.225, Y.228, Q.229 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:Q.50, B:S.114, B:S.114, B:Y.159, B:Y.228, B:Y.228, B:Q.229, B:Q.229 Water bridges: B:Y.112, B:Y.112, B:T.113 Salt bridges: B:K.15, B:K.15 pi-Stacking: B:Y.202, B:Y.228

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 4 residues within 4Å: Chain A: K.352, Y.387, L.388, S.391 Ligand excluded by PLIP

2 x FON: N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid(Non-covalent)

FON.3: 12 residues within 4Å: Chain A: S.80, F.83, K.85, I.86, V.87, N.99, I.132, D.133, H.134, G.135, I.136, D.137 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:F.83, A:K.85, A:V.87, A:V.87, A:V.87, A:N.99, A:D.137 Water bridges: A:D.133, A:T.138 FON.9: 19 residues within 4Å: Chain A: S.210, P.252 Chain B: S.80, F.83, D.84, K.85, I.86, V.87, N.99, M.111, H.130, I.132, D.133, G.135, I.136, D.137, Y.194, S.196, K.197 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:I.86, B:I.136 Hydrogen bonds: B:K.85, B:V.87, B:V.87, B:V.87, B:D.137, B:D.137, B:Y.194, B:Y.194, B:K.197 Water bridges: B:D.133, B:T.138, B:G.139

6 x NA: SODIUM ION(Non-functional Binders)

NA.4: 3 residues within 4Å: Chain A: S.90, F.92, N.93 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.90 NA.5: 5 residues within 4Å: Chain A: S.248, M.250, S.266, T.267, D.269 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.267, A:D.269 NA.6: 3 residues within 4Å: Chain A: Y.112, K.197, I.200 No protein-ligand interaction detected (PLIP) NA.7: 1 residues within 4Å: Chain B: I.64 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.64 Water bridges: B:I.64 NA.10: 5 residues within 4Å: Chain B: S.248, M.250, S.266, T.267, D.269 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.248, B:T.267 NA.11: 3 residues within 4Å: Chain B: Y.112, K.197, I.200 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.112, B:Y.112

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Woodford, C.R. et al., Molecular architecture of an N-formyltransferase from Salmonella enterica O60. J. Struct. Biol. (2017)

Release Date

2017-03-22

Peptides

Formyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Formyltransferase