SMTL ID : 4eh1.1 (1 other biounit)

Crystal Structure of the Flavohem-like-FAD/NAD Binding Domain of Nitric Oxide Dioxygenase from Vibrio cholerae O1 biovar El Tor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 18 residues within 4Å: Chain A: Y.39, R.55, Q.56, Y.57, S.58, S.71, V.72, K.73, E.75, N.81, G.83, L.84, V.85, S.86, V.124, T.127, E.233, F.235 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:Y.39, A:Q.56, A:F.235 Hydrogen bonds: A:Q.56, A:Q.56, A:Y.57, A:S.58, A:S.71, A:K.73, A:E.75, A:N.81, A:L.84, A:V.85, A:S.86 Water bridges: A:E.75 Salt bridges: A:R.55, A:R.55 pi-Stacking: A:Y.57, A:F.235, A:F.235 FAD.10: 18 residues within 4Å: Chain B: Y.39, R.55, Q.56, Y.57, S.58, S.71, V.72, K.73, E.75, G.83, L.84, V.85, S.86, V.124, T.127, E.233, F.235, H.238 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:Y.39, B:Q.56, B:F.235, B:F.235 Hydrogen bonds: B:Q.56, B:Q.56, B:Y.57, B:S.58, B:S.71, B:K.73, B:L.84, B:V.85, B:S.86, B:T.127, B:F.235 Water bridges: B:R.55 Salt bridges: B:R.55, B:R.55 pi-Stacking: B:Y.57, B:F.235, B:H.238, B:H.238

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 2 residues within 4Å: Chain A: D.97, S.98 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain A: R.113 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: C.150, N.151 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain B: N.151, R.178 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain B: K.73, G.123, V.124 Ligand excluded by PLIP

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

SO4.3: 5 residues within 4Å: Chain A: R.1, G.3, L.101, Y.102, A.103 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.101, A:A.103 Water bridges: A:R.1 Salt bridges: A:R.1 SO4.4: 4 residues within 4Å: Chain A: D.107, F.108, H.231, Y.232 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.232, A:Y.232 Water bridges: A:F.109

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: E.112, E.114, R.115, K.141, S.142 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.142 GOL.8: 5 residues within 4Å: Chain A: E.47, Y.88, N.92 Chain B: A.153, K.154 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.88, A:N.92, B:K.154 Water bridges: A:N.92, A:D.97 GOL.9: 5 residues within 4Å: Chain A: A.153, K.154 Chain B: E.47, Y.88, N.92 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:K.154, B:Y.88, B:Y.88 Water bridges: B:E.47 GOL.11: 7 residues within 4Å: Chain B: D.107, F.108, F.109, V.111, R.113, Y.205, H.231 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:F.109, B:F.109, B:V.111, B:R.113, B:R.113, B:Y.205, B:H.231 GOL.12: 7 residues within 4Å: Chain B: Y.39, I.40, G.41, Q.56, Y.102, A.103, A.105 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.56, B:A.103

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Crystal Structure of the Flavohem-like-FAD/NAD Binding Domain of Nitric Oxide Dioxygenase from Vibrio cholerae O1 biovar El Tor. To be Published

Release Date

2012-04-25

Peptides

Flavohemoprotein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Flavohemoprotein

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