SMTL ID : 4xcz.1

X-ray structure of the N-formyltransferase QdtF from Providencia alcalifaciens in complex with TDP-Qui3n and N5-THF

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

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.1: 16 residues within 4Å: Chain A: F.96, D.97, K.98, I.99, I.100, M.124, I.145, D.146, H.147, G.148, I.149, D.150, Y.207, S.209, K.210 Ligands: T3Q.2 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:I.99, A:I.99, A:K.210 Hydrogen bonds: A:K.98, A:I.100, A:I.100, A:I.100, A:D.150, A:Y.207, A:K.210, A:K.210 Water bridges: A:S.93, A:N.112, A:N.112 Salt bridges: A:K.210, A:K.210 FON.16: 16 residues within 4Å: Chain B: F.96, D.97, K.98, I.99, I.100, M.124, I.145, D.146, H.147, G.148, I.149, D.150, Y.207, S.209, K.210 Ligands: T3Q.17 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:I.99, B:I.99, B:K.210 Hydrogen bonds: B:K.98, B:I.100, B:I.100, B:I.100, B:D.150, B:Y.207, B:K.210, B:K.210 Water bridges: B:S.93, B:N.112, B:N.112, B:H.114, B:D.150 Salt bridges: B:K.210, B:K.210

4 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.2: 15 residues within 4Å: Chain A: K.28, E.95, F.96, H.114, G.123, M.124, Y.125, T.126, S.127, Y.172, Y.215, F.238, Y.241, Q.242 Ligands: FON.1 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:E.95, A:F.96, A:Y.125, A:Y.125, A:T.126, A:S.127, A:Y.241, A:Q.242, A:Q.242 Water bridges: A:N.29, A:N.29, A:E.95, A:E.95, A:E.95, A:H.114, A:H.114, A:G.123, A:Y.215, A:K.216, A:Y.241 Salt bridges: A:K.28 pi-Stacking: A:Y.215, A:Y.241 T3Q.3: 12 residues within 4Å: Chain A: W.325, I.329, I.330, Y.333, H.334, N.354, K.356, T.358, M.362, Y.363, D.366, Y.400 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:W.325, A:I.329, A:Y.333, A:Y.363, A:Y.363 Hydrogen bonds: A:W.325, A:H.334, A:N.354, A:T.358, A:Y.363, A:D.366, A:Y.400 Water bridges: A:M.362, A:K.365, A:K.365, A:Y.400 Salt bridges: A:K.356, A:K.356 pi-Stacking: A:W.325, A:Y.333 T3Q.17: 15 residues within 4Å: Chain B: K.28, E.95, F.96, H.114, G.123, M.124, Y.125, T.126, S.127, Y.172, Y.215, F.238, Y.241, Q.242 Ligands: FON.16 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:E.95, B:F.96, B:H.114, B:Y.125, B:Y.125, B:T.126, B:S.127, B:Y.172, B:Y.241, B:Y.241, B:Q.242, B:Q.242 Water bridges: B:N.29, B:N.29, B:E.95, B:E.95, B:E.95, B:G.123, B:G.123, B:K.216 Salt bridges: B:K.28 pi-Stacking: B:Y.215, B:Y.241 T3Q.18: 12 residues within 4Å: Chain B: W.325, I.329, I.330, Y.333, H.334, N.354, K.356, T.358, M.362, Y.363, D.366, Y.400 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:W.325, B:I.329, B:Y.333, B:Y.363, B:Y.363 Hydrogen bonds: B:W.325, B:Y.333, B:H.334, B:N.354, B:D.366, B:Y.400 Water bridges: B:M.362, B:K.365, B:K.365, B:D.391 Salt bridges: B:K.356, B:K.356 pi-Stacking: B:W.325, B:Y.333

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

NA.4: 5 residues within 4Å: Chain A: N.59, D.60, S.61, Q.63, S.65 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.59, A:S.61 Water bridges: A:N.59, A:S.61 NA.5: 2 residues within 4Å: Chain A: I.155, S.196 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.196, A:S.196 NA.6: 3 residues within 4Å: Chain A: Y.125, K.210, I.213 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.213 NA.8: 1 residues within 4Å: Chain A: K.216 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.216 NA.9: 2 residues within 4Å: Chain A: S.308, L.311 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.311 NA.19: 5 residues within 4Å: Chain B: N.59, D.60, S.61, Q.63, S.65 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.61, B:L.64 Water bridges: B:N.59, B:S.61 NA.20: 2 residues within 4Å: Chain B: I.155, S.196 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.196, B:S.196 NA.21: 3 residues within 4Å: Chain B: Y.125, K.210, I.213 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.125, B:Y.125 NA.23: 1 residues within 4Å: Chain B: K.216 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.216 NA.24: 2 residues within 4Å: Chain B: S.308, L.311 3 PLIP interactions: 3 interactions with chain B Water bridges: B:S.308, B:S.308, B:K.312

2 x K: POTASSIUM ION(Non-covalent)

K.7: 4 residues within 4Å: Chain B: S.261, S.263, S.279, T.280 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.261, B:S.279, B:T.280, H2O.23, H2O.28 K.22: 4 residues within 4Å: Chain A: S.261, S.263, S.279, T.280 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.261, A:S.279, A:T.280, H2O.2, H2O.7

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

CL.10: 5 residues within 4Å: Chain A: K.365, Y.400, M.401, N.404, N.406 Ligand excluded by PLIP CL.25: 5 residues within 4Å: Chain B: K.365, Y.400, M.401, N.404, N.406 Ligand excluded by PLIP

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

EDO.11: 4 residues within 4Å: Chain A: K.169, T.170, F.318, E.319 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.169, A:F.318 Water bridges: A:T.167, A:E.319, A:E.319, A:K.320 EDO.12: 2 residues within 4Å: Chain A: G.58, K.68 No protein-ligand interaction detected (PLIP) EDO.13: 5 residues within 4Å: Chain A: P.119, Q.157, E.199, Q.200, S.201 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.201 EDO.14: 4 residues within 4Å: Chain A: Y.274, N.291, L.310, K.312 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.291, A:K.312, A:K.312 Water bridges: A:Y.274, A:S.289 EDO.15: 4 residues within 4Å: Chain A: I.46, E.47, L.48, P.76 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.46, A:L.48, A:L.48 EDO.26: 4 residues within 4Å: Chain B: K.169, T.170, F.318, E.319 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.169, B:F.318 Water bridges: B:T.167, B:E.319, B:K.320 EDO.27: 2 residues within 4Å: Chain B: G.58, K.68 No protein-ligand interaction detected (PLIP) EDO.28: 5 residues within 4Å: Chain B: P.119, Q.157, E.199, Q.200, S.201 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.201 EDO.29: 4 residues within 4Å: Chain B: Y.274, N.291, L.310, K.312 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.291, B:K.312, B:K.312 Water bridges: B:S.289 EDO.30: 4 residues within 4Å: Chain B: I.46, E.47, L.48, P.76 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.46, B:L.48, B:L.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Woodford, C.R. et al., New Role for the Ankyrin Repeat Revealed by a Study of the N-Formyltransferase from Providencia alcalifaciens. Biochemistry (2015)

Release Date

2015-01-21

Peptides

TDP-3-aminoquinovose-N-formyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

TDP-3-aminoquinovose-N-formyltransferase

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