SMTL ID : 4xdt.1

Crystal structure of Treponema pallidum TP0796 Flavin trafficking protein, a bifunctional FMN transferase/FAD pyrophosphatase, N55Y mutant, FAD bound form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 30 residues within 4Å: Chain A: I.17, G.18, E.49, L.52, S.53, Y.55, A.96, F.97, N.98, P.99, L.101, V.105, D.159, G.161, A.162, A.164, K.165, L.168, S.240, E.244, R.245, H.256, I.257, I.258, P.260, D.284, T.288, V.292 Ligands: MG.2, MG.3 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:I.17, A:I.17, A:L.52, A:A.164 Hydrogen bonds: A:N.98, A:D.159, A:K.165, A:S.240, A:R.245, A:I.258, A:T.288 Water bridges: A:D.159, A:G.161, A:A.162, A:A.162, A:H.256 Salt bridges: A:K.165, A:K.165, A:H.256, A:H.256 pi-Stacking: A:Y.55

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain A: A.162, D.284, A.285, A.287, T.288 Ligands: FAD.1, MG.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:A.162, A:D.284, A:D.284, A:T.288, H2O.7 MG.3: 6 residues within 4Å: Chain A: A.162, K.165, V.238, D.284 Ligands: FAD.1, MG.2 5 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: A:D.284, FAD.1, H2O.4, H2O.5, H2O.7

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

NA.4: 3 residues within 4Å: Chain A: E.125, T.128, R.129 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.125, A:T.128, A:R.129 NA.5: 3 residues within 4Å: Chain A: H.267, T.268, V.292 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.267 Water bridges: A:H.267, A:H.267

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 6 residues within 4Å: Chain A: S.27, K.28, R.29, A.180, L.181, D.182 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.27, A:K.28, A:R.29, A:A.180 Water bridges: A:D.182, A:Y.199 ACT.7: 6 residues within 4Å: Chain A: D.182, L.195, G.196, L.197, R.233, D.234 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:D.182 ACT.8: 6 residues within 4Å: Chain A: R.24, L.185, K.198, W.212, N.213, V.214 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.185, A:W.212 Hydrogen bonds: A:N.213, A:N.213 Water bridges: A:R.24, A:K.198, A:K.198 Salt bridges: A:R.24, A:K.198 ACT.9: 8 residues within 4Å: Chain A: G.190, I.192, V.214, G.215, I.216, V.237, V.238, T.239 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.192 Hydrogen bonds: A:V.237, A:T.239, A:T.239

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

EDO.10: 9 residues within 4Å: Chain A: C.235, F.276, A.277, P.278, G.307, V.308, D.309, I.325 Ligands: EDO.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.309 EDO.11: 10 residues within 4Å: Chain A: S.231, V.232, R.233, C.235, F.276, D.309, G.324, I.325, R.328 Ligands: EDO.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.233, A:R.233, A:G.324 Water bridges: A:R.328 EDO.12: 6 residues within 4Å: Chain A: V.7, R.8, E.9, Y.26, Y.199, G.200 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.7 Water bridges: A:E.9, A:G.200 EDO.13: 7 residues within 4Å: Chain A: D.170, V.173, Q.174, F.193, P.278, R.279, S.280 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.174, A:P.278 EDO.14: 9 residues within 4Å: Chain A: S.93, G.94, G.95, A.96, D.259, P.260, V.261, V.292, L.293 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.94, A:D.259

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deka, R.K. et al., Evidence for Posttranslational Protein Flavinylation in the Syphilis Spirochete Treponema pallidum: Structural and Biochemical Insights from the Catalytic Core of a Periplasmic Flavin-Trafficking Protein. Mbio (2015)

Release Date

2015-10-14

Peptides

FAD:protein FMN transferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

FAD:protein FMN transferase

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