SMTL ID : 4xgx.1

Crystal structure of Escherichia coli Flavin trafficking protein, an FMN transferase, Y60N mutant, ADP-inhibited

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: T.166, D.280, D.283, T.284 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.166, A:D.280, A:D.280, A:T.284, H2O.5 MG.2: 5 residues within 4Å: Chain A: E.169, S.238, Y.239, R.240 Ligands: ADP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.169 MG.11: 4 residues within 4Å: Chain B: T.166, D.280, D.283, T.284 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.166, B:D.280, B:T.284, H2O.12 MG.12: 5 residues within 4Å: Chain B: E.169, S.238, Y.239, R.240 Ligands: ADP.13 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.169

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.3: 22 residues within 4Å: Chain A: A.101, M.102, D.103, I.104, V.106, V.110, D.163, S.165, T.166, E.169, G.237, S.238, Y.239, R.240, S.251, H.252, V.253, I.254, P.256, T.284, V.288 Ligands: MG.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:A.101, A:D.103, A:T.166, A:G.237, A:S.238, A:Y.239, A:R.240, A:I.254 Water bridges: A:S.165, A:R.240, A:S.251, A:T.284 Salt bridges: A:R.240, A:R.240 ADP.13: 24 residues within 4Å: Chain B: A.101, M.102, D.103, I.104, V.106, V.110, F.115, D.163, S.165, T.166, E.169, G.237, S.238, Y.239, R.240, H.252, V.253, I.254, D.255, P.256, T.284, V.288 Ligands: MG.12, NO3.15 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:A.101, B:D.103, B:S.238, B:Y.239, B:R.240, B:R.240, B:I.254 Water bridges: B:S.165, B:T.166, B:G.237

9 x NO3: NITRATE ION(Non-functional Binders)

NO3.4: 7 residues within 4Å: Chain A: T.90, R.93, I.94, K.97, E.278, W.282 Chain B: E.82 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.97, A:E.278, B:E.82 Water bridges: A:W.282 NO3.5: 4 residues within 4Å: Chain A: P.77, I.145, Q.147, Y.152 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.147 Water bridges: A:Y.152 NO3.6: 7 residues within 4Å: Chain A: H.231, I.272, A.273, P.274, F.326 Chain B: R.178, E.181 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.178, B:R.178, B:E.181, A:H.231 Water bridges: A:A.304, A:A.304 NO3.7: 6 residues within 4Å: Chain A: D.86, T.89, T.90, R.93 Chain B: D.86 Ligands: NO3.8 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.86, A:D.86, A:T.90 Water bridges: A:R.93, B:N.146, B:N.146 NO3.8: 6 residues within 4Å: Chain A: D.86 Chain B: D.86, T.89, T.90, R.93 Ligands: NO3.7 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:D.86, B:D.86, B:T.90, B:R.93 Water bridges: A:N.146, B:D.86 NO3.14: 4 residues within 4Å: Chain B: P.77, I.145, Q.147, Y.152 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.147 Water bridges: B:Y.152 NO3.15: 8 residues within 4Å: Chain B: T.166, S.236, G.237, V.253, D.283, T.284, M.287 Ligands: ADP.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.237, B:D.283, B:T.284 NO3.16: 7 residues within 4Å: Chain A: E.82 Chain B: T.90, R.93, I.94, K.97, E.278, W.282 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Water bridges: A:E.82, B:W.282, B:W.282 Hydrogen bonds: B:K.97, B:E.278 NO3.17: 7 residues within 4Å: Chain A: P.274 Chain B: D.174, A.177, R.178, E.181, R.199 Ligands: EDO.18 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.181 Water bridges: B:N.197, B:N.197, B:R.199

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

EDO.9: 8 residues within 4Å: Chain A: D.227, I.228, N.229, H.231, F.326 Chain B: S.186, R.199, G.200 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:G.200 Hydrogen bonds: A:D.227, A:H.231 EDO.10: 7 residues within 4Å: Chain A: D.174, A.177, R.178, E.181 Chain B: H.231, P.274 Ligands: EDO.19 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.178, A:E.181 EDO.18: 5 residues within 4Å: Chain B: Y.171, D.174, H.175, R.178 Ligands: NO3.17 No protein-ligand interaction detected (PLIP) EDO.19: 11 residues within 4Å: Chain A: E.181, Y.188, S.198, R.199, G.230, H.231 Chain B: R.199, N.229, G.230, H.231 Ligands: EDO.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.230, A:G.230

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deka, R.K. et al., Molecular insights into the enzymatic diversity of flavin-trafficking protein (Ftp; formerly ApbE) in flavoprotein biogenesis in the bacterial periplasm. Microbiologyopen (2016)

Release Date

2015-12-16

Peptides

FAD:protein FMN transferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

FAD:protein FMN transferase