SMTL ID : 1z44.1 (1 other biounit)

Crystal structure of oxidized YqjM from Bacillus subtilis complexed with p-nitrophenol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-tetramer

Ligands

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: R.318, K.322 Chain B: R.312 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:R.318, B:E.309, B:R.312 Salt bridges: A:R.318 SO4.4: 3 residues within 4Å: Chain A: R.312 Chain B: R.318, K.322 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Water bridges: B:R.318, B:R.318, A:R.312 Salt bridges: B:R.318, B:K.322 SO4.8: 3 residues within 4Å: Chain C: R.318, K.322 Chain D: R.312 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Water bridges: D:E.309, D:R.312, C:R.318 Salt bridges: C:R.318 SO4.11: 3 residues within 4Å: Chain C: R.312 Chain D: R.318, K.322 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain D Water bridges: C:R.312, D:R.318, D:R.318 Salt bridges: D:R.318, D:K.322

4 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 17 residues within 4Å: Chain A: S.23, P.24, M.25, C.26, A.60, Q.102, H.164, H.167, R.215, V.283, G.284, M.285, I.306, G.307, R.308 Chain B: R.336 Ligands: NPO.3 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:R.308 Hydrogen bonds: A:S.23, A:S.23, A:P.24, A:C.26, A:A.60, A:Q.102, A:Q.102, A:R.215, A:R.215, A:G.284, A:G.307, A:R.308 Water bridges: A:I.286, A:I.286, A:R.308, A:R.308, A:E.309, A:E.309 Salt bridges: A:R.308 FMN.5: 17 residues within 4Å: Chain A: R.336 Chain B: S.23, P.24, M.25, C.26, A.60, Q.102, H.164, H.167, R.215, V.283, G.284, M.285, I.306, G.307, R.308 Ligands: NPO.6 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:R.308 Hydrogen bonds: B:S.23, B:S.23, B:P.24, B:C.26, B:A.60, B:Q.102, B:Q.102, B:R.215, B:R.215, B:G.284, B:G.307, B:R.308 Water bridges: B:I.286, B:I.286, B:E.309 Salt bridges: B:R.308 FMN.9: 17 residues within 4Å: Chain C: S.23, P.24, M.25, C.26, A.60, Q.102, H.164, H.167, R.215, V.283, G.284, M.285, I.306, G.307, R.308 Chain D: R.336 Ligands: NPO.10 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:R.308 Hydrogen bonds: C:S.23, C:S.23, C:P.24, C:C.26, C:A.60, C:Q.102, C:Q.102, C:H.167, C:R.215, C:R.215, C:G.284, C:G.307, C:R.308 Water bridges: C:I.286, C:I.286, C:R.308, C:R.308, C:E.309, C:E.309 Salt bridges: C:R.308 FMN.12: 17 residues within 4Å: Chain C: R.336 Chain D: S.23, P.24, M.25, C.26, A.60, Q.102, H.164, H.167, R.215, V.283, G.284, M.285, I.306, G.307, R.308 Ligands: NPO.13 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:R.308 Hydrogen bonds: D:S.23, D:S.23, D:P.24, D:C.26, D:A.60, D:Q.102, D:Q.102, D:H.167, D:R.215, D:R.215, D:G.284, D:G.307, D:R.308 Water bridges: D:I.286, D:I.286, D:E.309 Salt bridges: D:R.308

6 x NPO: P-NITROPHENOL(Covalent)(Non-covalent)

NPO.3: 8 residues within 4Å: Chain A: C.26, Y.28, I.69, H.164, H.167, Y.169 Chain B: R.336 Ligands: FMN.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.69, A:Y.169 Hydrogen bonds: A:H.167 NPO.6: 8 residues within 4Å: Chain A: R.336 Chain B: C.26, Y.28, I.69, H.164, H.167, Y.169 Ligands: FMN.5 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.69, B:Y.169 Hydrogen bonds: B:H.164 NPO.7: 8 residues within 4Å: Chain A: P.39, M.42, A.43, I.46 Chain B: P.39, M.42, A.43, I.46 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.39 NPO.10: 8 residues within 4Å: Chain C: C.26, Y.28, I.69, H.164, H.167, Y.169 Chain D: R.336 Ligands: FMN.9 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.69, C:Y.169 Hydrogen bonds: C:H.167, C:Y.169 NPO.13: 8 residues within 4Å: Chain C: R.336 Chain D: C.26, Y.28, I.69, H.164, H.167, Y.169 Ligands: FMN.12 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:I.69, D:Y.169 Hydrogen bonds: D:H.164, D:H.167 NPO.14: 8 residues within 4Å: Chain C: P.39, M.42, A.43, I.46 Chain D: P.39, M.42, A.43, I.46 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:P.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kitzing, K. et al., The 1.3 A Crystal Structure of the Flavoprotein YqjM Reveals a Novel Class of Old Yellow Enzymes. J.Biol.Chem. (2005)

Release Date

2005-05-17

Peptides

Probable NADH-dependent flavin oxidoreductase yqjM: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Probable NADH-dependent flavin oxidoreductase yqjM

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