SMTL ID : 5jv4.2 (2 other biounits)

Structure of F420 binding protein, MSMEG_6526, from Mycobacterium smegmatis with F420 bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x F42: COENZYME F420(Non-covalent)

F42.1: 13 residues within 4Å: Chain A: D.91, L.100, W.101, W.102, W.152 Chain B: P.43, V.44, V.45, T.62, A.63, V.64, D.65 Ligands: MPD.3 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.43, A:W.152 Hydrogen bonds: B:V.45, B:A.63, B:D.65, A:D.91 Water bridges: B:P.43 F42.2: 14 residues within 4Å: Chain A: H.40, V.42, P.43, V.44, V.45, T.62, A.63, V.64, D.65, R.76 Chain B: L.100, W.102, W.152 Ligands: MRD.5 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:P.43, B:L.100, B:W.152 Hydrogen bonds: A:P.43, A:V.45, A:A.63, A:D.65, A:Y.132 Salt bridges: A:H.40 Water bridges: B:H.92, B:H.92

3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 6 residues within 4Å: Chain A: W.97, W.152 Chain B: V.45, D.65, Y.132 Ligands: F42.1 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.45, A:W.97, A:W.152 Hydrogen bonds: B:D.65 Water bridges: B:Y.132 MPD.4: 5 residues within 4Å: Chain A: P.57, V.108, E.145, V.146, S.147 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.57, A:V.108, A:E.145 MPD.6: 5 residues within 4Å: Chain B: D.17, A.18, A.21, W.101, S.151 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.21, B:W.101 Hydrogen bonds: B:S.151

1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.5: 7 residues within 4Å: Chain A: V.45, D.65, Y.132, V.135 Chain B: W.97, W.152 Ligands: F42.2 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.45, A:V.135, B:W.152 Hydrogen bonds: A:Y.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, B.M. et al., Structure of F420 binding protein, MSMEG_6526, from Mycobacterium smegmatis with F420 bound. To Be Published

Release Date

2017-08-09

Peptides

Pyridoxamine 5'-phosphate oxidase-like FMN-binding protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
E

Pyridoxamine 5'-phosphate oxidase-like FMN-binding protein

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