SMTL ID : 5uik.1

X-ray structure of the FdtF formyltransferase from salmonella enteric O60 in complex with TDP-Fuc3N and folinic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

4 x T3F: (3R,4S,5R,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)

T3F.1: 12 residues within 4Å: Chain A: W.312, I.316, V.317, Y.320, H.321, N.341, K.343, T.345, Y.350, K.352, D.353, Y.387 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.312, A:I.316, A:Y.320, A:Y.350, A:Y.350 Hydrogen bonds: A:N.341, A:K.352, A:K.352, A:D.353 Salt bridges: A:K.343, A:K.343 pi-Stacking: A:W.312, A:Y.320 T3F.3: 13 residues within 4Å: Chain A: K.15, E.82, F.83, G.110, M.111, Y.112, S.114, Y.159, Y.202, F.225, Y.228, Q.229 Ligands: FON.2 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:Y.228 Hydrogen bonds: A:E.82, A:F.83, A:G.110, A:Y.112, A:S.114, A:Q.229, A:Q.229 Water bridges: A:K.15, A:N.16, A:N.99, A:H.101, A:H.101, A:H.101, A:H.101, A:T.113, A:T.113, A:Y.228, A:Y.228 Salt bridges: A:K.15 pi-Stacking: A:Y.202, A:Y.228 T3F.5: 10 residues within 4Å: Chain B: W.312, Y.320, H.321, N.341, K.343, T.345, Y.350, K.352, D.353, Y.387 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:W.312, B:Y.320, B:Y.320, B:Y.350, B:Y.350 Hydrogen bonds: B:N.341, B:T.345, B:T.345, B:Y.350, B:K.352, B:D.353 Water bridges: B:D.378, B:Y.387 Salt bridges: B:K.343, B:K.343 pi-Stacking: B:W.312, B:Y.320 T3F.7: 15 residues within 4Å: Chain B: K.15, N.40, E.82, F.83, G.110, M.111, Y.112, T.113, S.114, Y.159, Y.202, F.225, Y.228, Q.229 Ligands: FON.6 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.228 Hydrogen bonds: B:E.82, B:F.83, B:G.110, B:Y.112, B:S.114, B:Q.229, B:Q.229 Water bridges: B:N.99, B:T.113, B:T.113 Salt bridges: B:K.15 pi-Stacking: B:Y.202, B:Y.228

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.2: 13 residues within 4Å: Chain A: F.83, D.84, K.85, I.86, V.87, I.132, D.133, H.134, G.135, I.136, D.137, K.197 Ligands: T3F.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.86 Hydrogen bonds: A:K.85, A:V.87, A:V.87, A:V.87, A:D.137 Water bridges: A:N.99, A:N.99, A:H.101, A:T.138 FON.6: 13 residues within 4Å: Chain B: F.83, D.84, K.85, I.86, V.87, I.132, D.133, H.134, G.135, I.136, D.137, K.197 Ligands: T3F.7 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.86 Hydrogen bonds: B:K.85, B:V.87, B:V.87, B:V.87, B:N.99, B:D.137, B:K.197, B:K.197 Water bridges: B:T.138, B:Y.194

3 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.267, A:D.269 Water bridges: A:S.248, A:S.266 NA.8: 4 residues within 4Å: Chain B: S.248, M.250, S.266, T.267 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.267, B:D.269 Water bridges: B:S.248, B:S.266 NA.9: 4 residues within 4Å: Chain B: Y.112, K.197, I.200, D.201 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: 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

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