SMTL ID : 5uij.1

X-ray structure of The FdtF N-formyltransferase from Salmonella enteric O60 in complex with TDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

4 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:S.114, A:Q.229, A:Q.229 Water bridges: A:K.15, A:K.15, A:N.16, A:E.82, A:Y.112, A:T.113, A:S.114, A:Y.159, A:Y.202 Salt bridges: A:K.15, A:K.15 pi-Stacking: A:Y.202, A:Y.228 TYD.2: 9 residues within 4Å: Chain A: W.312, I.316, V.317, Y.320, H.321, N.341, K.343, T.345, Y.350 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:W.312, A:I.316, A:Y.320, A:Y.320, A:Y.350 Hydrogen bonds: A:Y.320, A:N.341, A:T.345, A:Y.350, A:Y.350 Water bridges: A:H.321 Salt bridges: A:K.343, A:K.343 pi-Stacking: A:W.312, A:Y.320 TYD.7: 10 residues within 4Å: Chain B: 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 B Hydrogen bonds: B:E.82, B:S.114, B:S.114, B:Y.159, B:Y.159, B:Q.229, B:Q.229 Water bridges: B:K.15, B:K.15, B:N.16, B:Y.112, B:T.113 Salt bridges: B:K.15, B:K.15 pi-Stacking: B:Y.202, B:Y.228 TYD.8: 10 residues within 4Å: Chain B: Y.310, W.312, I.316, V.317, Y.320, H.321, N.341, K.343, T.345, Y.350 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:W.312, B:I.316, B:Y.320, B:Y.320, B:Y.350 Hydrogen bonds: B:N.341, B:Y.350 Water bridges: B:Y.320, B:Y.342, B:T.345, B:K.380 pi-Stacking: B:W.312, B:Y.320

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 2 residues within 4Å: Chain A: A.402, F.403 No protein-ligand interaction detected (PLIP)

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

NA.4: 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.5: 3 residues within 4Å: Chain A: Y.112, K.197, I.200 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.200 NA.6: 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.9: 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:I.200 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:T.267, B:T.267

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

Related Entries With Identical Sequence