SMTL ID : 1t0i.2 (1 other biounit)

YLR011wp, a Saccharomyces cerevisiae NA(D)PH-dependent FMN reductase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.134, E.138 Chain C: D.134, E.138 Ligands: CA.5 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:D.134, C:E.138, A:E.138, H2O.3, H2O.7 CA.2: 2 residues within 4Å: Chain A: D.134 Chain C: E.138 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: C:E.138, A:D.134, H2O.1, H2O.1, H2O.5 CA.5: 5 residues within 4Å: Chain A: D.134, E.138 Chain C: D.134, E.138 Ligands: CA.1 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:E.138, A:D.134, A:E.138, H2O.3, H2O.7 CA.6: 2 residues within 4Å: Chain A: E.138 Chain C: D.134 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: C:D.134, A:E.138, H2O.1, H2O.5, H2O.6

4 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.3: 16 residues within 4Å: Chain A: S.9, R.11, R.14, V.15, C.16, P.93, Q.94, Y.95, N.96, W.97, Y.124, G.125, G.126, V.157 Chain B: I.60, D.108 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.95, A:Y.95, B:I.60, B:I.60 Hydrogen bonds: A:S.9, A:R.11, A:V.15, A:C.16, A:Q.94, A:Y.95, A:Y.95, A:N.96, A:W.97, A:Y.124, A:G.126 Water bridges: A:H.127, A:G.158 Salt bridges: A:R.11 FMN.4: 17 residues within 4Å: Chain A: I.60, D.108 Chain B: S.9, R.11, R.14, V.15, C.16, P.93, Q.94, Y.95, N.96, W.97, Y.124, G.125, G.126, V.157, I.160 20 PLIP interactions: 18 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.95, B:Y.95, B:Y.95, B:Y.95, A:I.60, A:D.108 Hydrogen bonds: B:S.9, B:R.11, B:V.15, B:C.16, B:Q.94, B:Y.95, B:N.96, B:W.97, B:G.126 Water bridges: B:H.127, B:G.158, B:G.158, B:G.158 Salt bridges: B:R.11 FMN.7: 16 residues within 4Å: Chain C: S.9, R.11, R.14, V.15, C.16, P.93, Q.94, Y.95, N.96, W.97, Y.124, G.125, G.126, V.157 Chain D: I.60, D.108 18 PLIP interactions: 16 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:Y.95, C:Y.95, D:I.60, D:I.60 Hydrogen bonds: C:S.9, C:R.11, C:V.15, C:C.16, C:Q.94, C:Y.95, C:Y.95, C:N.96, C:W.97, C:Y.124, C:G.126 Water bridges: C:H.127, C:G.158 Salt bridges: C:R.11 FMN.8: 17 residues within 4Å: Chain C: I.60, D.108 Chain D: S.9, R.11, R.14, V.15, C.16, P.93, Q.94, Y.95, N.96, W.97, Y.124, G.125, G.126, V.157, I.160 20 PLIP interactions: 2 interactions with chain C, 18 interactions with chain D Hydrophobic interactions: C:I.60, C:D.108, D:Y.95, D:Y.95, D:Y.95, D:Y.95 Hydrogen bonds: D:S.9, D:R.11, D:V.15, D:C.16, D:Q.94, D:Y.95, D:N.96, D:W.97, D:G.126 Water bridges: D:H.127, D:G.158, D:G.158, D:G.158 Salt bridges: D:R.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liger, D. et al., Crystal Structure and Functional Characterization of Yeast YLR011wp, an Enzyme with NAD(P)H-FMN and Ferric Iron Reductase Activities. J.Biol.Chem. (2004)

Release Date

2004-06-22

Peptides

YLR011wp: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

YLR011wp

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