SMTL ID : 5jv4.1 (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: 14 residues within 4Å: Chain A: V.42, P.43, V.44, V.45, T.62, A.63, V.64, D.65 Chain B: D.91, L.100, W.101, W.102, W.152 Ligands: MPD.2 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:V.45, A:A.63, A:D.65, B:D.91, B:W.152 Water bridges: A:H.40, A:P.43, A:Y.132 Hydrophobic interactions: B:W.152 F42.4: 25 residues within 4Å: Chain A: D.91, L.100, W.101, W.102, R.104, R.148, A.150, W.152 Chain B: H.40, V.42, P.43, V.44, V.45, T.62, A.63, V.64, D.65, K.67, R.68, K.69, T.70, T.71, L.74, R.75, R.76 31 PLIP interactions: 7 interactions with chain A, 24 interactions with chain B Hydrophobic interactions: A:W.102, A:W.152, B:P.43, B:K.67, B:T.71 Hydrogen bonds: A:D.91, A:R.104, B:V.45, B:A.63, B:D.65, B:K.67, B:K.69, B:T.70, B:T.71, B:R.75, B:R.75, B:R.76 Water bridges: A:R.148, B:A.63, B:D.65, B:R.75, B:R.76, B:R.76, B:R.76 Salt bridges: A:R.104, A:R.148, B:H.40, B:R.75, B:R.76 pi-Cation interactions: B:K.67, B:K.67

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

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

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

NA.3: 2 residues within 4Å: Chain A: H.49, H.52 No protein-ligand interaction detected (PLIP)

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
A

B
D

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

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