SMTL ID : 3gbh.1 (1 other biounit)

CRYSTAL STRUCTURE OF A PUTATIVE NAD(P)H:FMN OXIDOREDUCTASE (SE1966) FROM STAPHYLOCOCCUS EPIDERMIDIS ATCC 12228 AT 2.00 A RESOLUTION

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 22 residues within 4Å: Chain A: R.18, K.19, S.20, K.22, N.75, Q.78, N.162, P.163, I.164, G.165, G.166, S.201, R.203 Chain B: P.46, S.47, S.48, N.50, I.141, D.142, L.145 Ligands: UNL.5, GOL.7 21 PLIP interactions: 17 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:P.163, B:I.141, B:L.145 Hydrogen bonds: A:S.20, A:S.20, A:S.20, A:S.20, A:K.22, A:K.22, A:N.75, A:N.75, A:Q.78, A:N.162, A:G.165, A:G.166, A:S.201, A:S.201, B:S.47, B:V.49 Salt bridges: A:R.18, A:R.203 FMN.4: 23 residues within 4Å: Chain A: P.46, S.47, S.48, V.49, N.50, I.141, D.142, L.145 Chain B: R.18, K.19, S.20, K.22, N.75, Q.78, N.162, P.163, I.164, G.165, G.166, S.201, R.203 Ligands: UNL.2, GOL.3 22 PLIP interactions: 5 interactions with chain A, 17 interactions with chain B Hydrophobic interactions: A:P.46, A:I.141, A:L.145, B:P.163 Hydrogen bonds: A:S.47, A:V.49, B:S.20, B:S.20, B:S.20, B:S.20, B:K.22, B:K.22, B:N.75, B:N.75, B:Q.78, B:N.162, B:G.165, B:G.166, B:S.201, B:S.201 Salt bridges: B:R.18, B:R.203 FMN.11: 22 residues within 4Å: Chain C: R.18, K.19, S.20, K.22, N.75, Q.78, N.162, P.163, I.164, G.165, G.166, S.201, R.203 Chain D: P.46, S.47, S.48, N.50, I.141, D.142, L.145 Ligands: UNL.16, GOL.17 23 PLIP interactions: 18 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:P.163, D:P.46, D:I.141, D:L.145 Hydrogen bonds: C:S.20, C:S.20, C:S.20, C:S.20, C:K.22, C:K.22, C:N.75, C:N.75, C:Q.78, C:N.162, C:G.165, C:G.166, C:S.201, C:S.201, D:S.47, D:V.49 Water bridges: C:R.203 Salt bridges: C:R.18, C:R.203 FMN.15: 23 residues within 4Å: Chain C: P.46, S.47, S.48, N.50, I.141, D.142, L.145 Chain D: R.18, K.19, S.20, K.22, N.75, Q.78, N.162, P.163, I.164, G.165, G.166, L.187, S.201, R.203 Ligands: UNL.12, GOL.14 22 PLIP interactions: 18 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:P.163, D:L.187, C:I.141, C:L.145 Hydrogen bonds: D:S.20, D:S.20, D:S.20, D:S.20, D:K.22, D:K.22, D:N.75, D:N.75, D:Q.78, D:N.162, D:G.165, D:G.166, D:S.201, D:S.201, C:S.47, C:V.49 Salt bridges: D:R.18, D:R.203

4 x UNL: UNKNOWN LIGAND

UNL.2: 8 residues within 4Å: Chain A: S.48, V.49, W.122, Y.126 Chain B: K.22, G.166 Ligands: GOL.3, FMN.4 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:V.49, A:Y.126, B:K.22, B:K.22 Water bridges: A:S.48 UNL.5: 4 residues within 4Å: Chain B: S.48, V.49 Ligands: FMN.1, GOL.7 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Water bridges: A:K.22, A:K.22, B:S.48, B:S.48, B:Y.126 Hydrogen bonds: B:V.49 UNL.12: 5 residues within 4Å: Chain C: S.48, V.49, W.122 Ligands: GOL.14, FMN.15 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Water bridges: D:G.165, C:S.48, C:S.48 Hydrogen bonds: C:V.49 UNL.16: 6 residues within 4Å: Chain C: G.166 Chain D: S.48, V.49, W.122 Ligands: FMN.11, GOL.17 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:V.49, D:Y.126, D:Y.126 Water bridges: D:S.48

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: V.49, N.50, Y.102, M.111 Ligands: UNL.2, FMN.4 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:N.50, B:K.22 GOL.6: 4 residues within 4Å: Chain B: R.7, I.8, N.9, D.10 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.7, B:N.9, B:N.9, B:D.10 GOL.7: 6 residues within 4Å: Chain B: V.49, N.50, Y.102, M.111 Ligands: FMN.1, UNL.5 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.50 GOL.13: 5 residues within 4Å: Chain C: R.7, I.8, N.9, D.10, E.13 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.7, C:N.9, C:D.10 Water bridges: C:N.9 GOL.14: 6 residues within 4Å: Chain C: V.49, N.50, Y.102, M.111 Ligands: UNL.12, FMN.15 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Water bridges: D:K.22, D:K.22, C:N.50 GOL.17: 5 residues within 4Å: Chain D: V.49, Y.102, M.111 Ligands: FMN.11, UNL.16 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Water bridges: C:K.22, C:K.22, D:N.50

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.8: 8 residues within 4Å: Chain A: R.55, Y.178, Y.183 Chain B: D.207, D.208, V.209, R.210, E.211 No protein-ligand interaction detected (PLIP) PGE.18: 7 residues within 4Å: Chain C: D.208, V.209, R.210, E.211 Chain D: R.55, Y.178, Y.183 No protein-ligand interaction detected (PLIP)

5 x CA: CALCIUM ION(Non-covalent)

CA.9: 1 residues within 4Å: Chain B: D.114 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.114, H2O.4 CA.10: 2 residues within 4Å: Chain B: D.104, E.107 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.104, B:E.107, B:E.107, H2O.6, H2O.12 CA.19: 1 residues within 4Å: Chain D: D.114 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.114, H2O.11 CA.20: 2 residues within 4Å: Chain D: D.104, E.107 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.104, D:E.107, H2O.8, H2O.13, H2O.14 CA.21: 2 residues within 4Å: Chain D: D.179, D.181 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.179, D:D.179, D:D.181

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of putative NAD(P)H:FMN oxidoreductase (NP_765521.1) from Staphylococcus epidermidis ATCC 12228 at 2.00 A resolution. To be published

Release Date

2009-03-03

Peptides

NAD(P)H-flavin oxidoreductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

NAD(P)H-flavin oxidoreductase

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