SMTL ID : 4xdr.1

Crystal structure of Treponema pallidum TP0796 Flavin trafficking protein, a bifunctional FMN transferase/FAD pyrophosphatase, D284A mutant, ADN bound form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: H.267, T.268, V.292 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.267, H2O.5, H2O.7, H2O.7, H2O.8

1 x ADN: ADENOSINE(Non-covalent)

ADN.2: 18 residues within 4Å: Chain A: A.96, F.97, N.98, P.99, L.101, V.105, D.159, G.161, A.162, R.245, H.256, I.257, I.258, P.260, T.288, V.292 Ligands: EDO.9, EDO.11 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.98, A:D.159, A:H.256, A:I.258, A:I.258 Water bridges: A:G.161, A:A.162, A:R.245

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

ACT.3: 6 residues within 4Å: Chain A: R.24, L.185, K.198, W.212, N.213, V.214 7 PLIP interactions: 7 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 Salt bridges: A:R.24, A:K.198 ACT.4: 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.5: 4 residues within 4Å: Chain A: R.8, E.9, Y.26, G.200 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.9 Water bridges: A:Y.26, A:Y.26 ACT.6: 9 residues within 4Å: Chain A: R.85, F.89, A.277, P.278, R.279, D.282, F.305, G.307, V.308 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.308 Water bridges: A:R.279 Salt bridges: A:R.85, A:R.279 ACT.7: 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 ACT.8: 4 residues within 4Å: Chain A: S.11, R.12, A.13, R.22 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.11, A:R.12 Salt bridges: A:R.22

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

EDO.9: 14 residues within 4Å: Chain A: A.162, K.165, N.191, V.238, T.239, S.240, G.241, E.244, H.256, I.257, A.284, A.287, T.288 Ligands: ADN.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.165, A:N.191, A:S.240 Water bridges: A:A.162 EDO.10: 5 residues within 4Å: Chain A: D.182, L.195, G.196, R.233, D.234 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.197 EDO.11: 9 residues within 4Å: Chain A: V.105, W.108, N.109, F.112, R.245, H.255, H.256, I.258 Ligands: ADN.2 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.109 EDO.12: 9 residues within 4Å: Chain A: C.235, F.276, A.277, P.278, G.307, V.308, D.309, G.324, I.325 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.276 EDO.13: 8 residues within 4Å: Chain A: G.102, A.103, K.106, L.107, A.126, R.129, G.155, Q.157 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.103, A:R.129, A:R.129

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