SMTL ID : 5uim.1

X-ray structure of the FdtF N-formyltransferase from salmonella enteric O60 in complex with folinic acid and TDP-Qui3N

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

3 x T3Q: [(3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-methyloxan-2-yl][hydroxy-[[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate(Non-covalent)

T3Q.1: 15 residues within 4Å: Chain A: K.15, E.82, F.83, D.84, H.101, G.110, M.111, Y.112, T.113, S.114, Y.159, Y.202, F.225, Y.228, Q.229 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:E.82, A:F.83, A:Y.112, A:Y.112, A:T.113, A:S.114, A:Y.228, A:Y.228, A:Q.229, A:Q.229 Water bridges: A:K.15, A:K.15, A:N.16, A:E.82, A:E.82, A:N.99, A:H.101 Salt bridges: A:K.15 pi-Stacking: A:Y.202, A:Y.228 T3Q.2: 14 residues within 4Å: Chain A: W.312, I.316, V.317, Y.320, H.321, N.341, K.343, T.345, M.349, Y.350, K.352, D.353, K.380, Y.387 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:W.312, A:I.316, A:Y.320, A:Y.350, A:Y.350 Hydrogen bonds: A:W.312, A:N.341, A:T.345, A:Y.350, A:K.352, A:K.352, A:D.353, A:K.380, A:Y.387 Salt bridges: A:K.343, A:K.343 pi-Stacking: A:W.312, A:Y.320 T3Q.6: 13 residues within 4Å: Chain B: W.312, I.316, V.317, Y.320, H.321, N.341, K.343, T.345, M.349, Y.350, K.352, D.353, Y.387 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:W.312, B:I.316, B:Y.320, B:Y.320, B:Y.350 Hydrogen bonds: B:W.312, B:N.341, B:K.352, B:K.352, B:D.353, B:Y.387 Water bridges: B:Y.387, B:Y.387 pi-Stacking: B:W.312, B:Y.320

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

NA.3: 3 residues within 4Å: Chain A: Y.112, K.197, I.200 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.197 NA.4: 6 residues within 4Å: Chain A: S.248, M.250, S.266, T.267, D.269, D.271 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.267, A:D.271 NA.8: 4 residues within 4Å: Chain B: S.248, M.250, S.266, T.267 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.248 Water bridges: B:T.267 NA.10: 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

1 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.5: 18 residues within 4Å: Chain A: S.210, K.251 Chain B: S.80, F.83, D.84, K.85, I.86, V.87, N.99, M.111, I.132, D.133, G.135, I.136, D.137, Y.194, S.196, K.197 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:I.86, B:I.136, B:I.136 Hydrogen bonds: B:K.85, B:V.87, B:V.87, B:V.87, B:N.99, B:D.137, B:D.137, B:Y.194, B:Y.194, B:Y.194, B:K.197 Water bridges: B:D.133, B:T.138

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

TYD.7: 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 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:Y.228 Hydrogen bonds: B:Q.50, B:Q.50, B:S.114, B:S.114, B:Q.229, B:Q.229 Water bridges: B:N.16, B:Y.112, B:Y.112, B:T.113, B:S.114, B:Y.228, B:Y.228 Salt bridges: B:K.15, B:K.15 pi-Stacking: B:Y.202, B:Y.228

1 x K: POTASSIUM ION(Non-covalent)

K.9: 1 residues within 4Å: Chain B: I.64 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:I.64, H2O.5, H2O.6, H2O.8, H2O.9

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