SMTL ID : 3e4v.1

Crystal structure of NADH:FMN oxidoreductase like protein in complex with FMN (YP_544701.1) from METHYLOBACILLUS FLAGELLATUS KT at 1.40 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 28 residues within 4Å: Chain A: I.20, N.33, L.34, M.35, T.36, M.37, G.38, F.39, I.53, I.54, G.55, W.57, D.58, Y.59, S.60, V.84, I.86, G.87, N.88, C.89, S.90, G.91, K.96, H.159 Chain B: M.178, K.180, W.181 Ligands: GOL.9 20 PLIP interactions: 18 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:T.36 Hydrogen bonds: A:N.33, A:T.36, A:T.36, A:G.38, A:F.39, A:I.53, A:G.55, A:D.58, A:D.58, A:Y.59, A:S.60, A:S.60, A:G.87, A:C.89, A:S.90, A:G.91, B:K.180 Salt bridges: A:K.96, B:K.180 FMN.7: 29 residues within 4Å: Chain A: M.178, K.180, W.181 Chain B: I.20, N.33, L.34, M.35, T.36, M.37, G.38, F.39, I.53, I.54, G.55, W.57, D.58, Y.59, S.60, V.84, I.86, G.87, N.88, C.89, S.90, G.91, K.96, H.159, F.165 Ligands: GOL.4 20 PLIP interactions: 18 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:T.36, B:F.165 Hydrogen bonds: B:N.33, B:T.36, B:T.36, B:G.38, B:F.39, B:I.53, B:G.55, B:D.58, B:Y.59, B:S.60, B:S.60, B:G.87, B:C.89, B:S.90, B:G.91, A:K.180 Salt bridges: B:K.96, A:K.180

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

NA.2: 2 residues within 4Å: Chain A: H.40 Chain B: H.40 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Water bridges: A:H.40, B:H.40, B:H.40 Hydrogen bonds: B:H.40 NA.8: 1 residues within 4Å: Chain B: D.111 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.111

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

ACT.3: 5 residues within 4Å: Chain A: G.175, M.178, W.181, R.182 Chain B: D.162 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.162 Salt bridges: A:R.182

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: H.45, M.178, W.181 Chain B: W.57 Ligands: FMN.7 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:W.181, B:W.57 Water bridges: A:H.45, B:H.159, B:H.159 GOL.5: 3 residues within 4Å: Chain A: L.94, H.99 Ligands: PEG.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.99 GOL.9: 6 residues within 4Å: Chain A: W.57 Chain B: H.45, M.178, W.181 Ligands: FMN.1, GOL.10 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:H.159, B:H.45 Hydrogen bonds: B:W.181 GOL.10: 7 residues within 4Å: Chain A: F.39, I.53, W.57 Chain B: M.43, Q.44, H.45 Ligands: GOL.9 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.45, B:H.45 Water bridges: B:E.46

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 2 residues within 4Å: Chain A: A.93 Ligands: GOL.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of NADH:FMN oxidoreductase like protein in complex with FMN (YP_544701.1) from METHYLOBACILLUS FLAGELLATUS KT at 1.40 A resolution. To be published

Release Date

2008-09-02

Peptides

NADH:FMN oxidoreductase like protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NADH:FMN oxidoreductase like protein