SMTL ID : 5gv8.1

Structure of NADH-cytochrome b5 reductase refined with the multipolar atomic model at 0.78A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 0.78 Å

Oligo State

monomer

Ligands

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

FAD.1: 28 residues within 4Å: Chain A: H.49, V.61, R.63, P.64, Y.65, T.66, V.80, I.81, K.82, Y.84, F.85, T.88, H.89, F.92, G.95, G.96, K.97, M.98, S.99, Q.100, T.153, T.156, P.157, Q.182, C.245, F.272 Ligands: GOL.4, GOL.5 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:P.64, A:P.157 Hydrogen bonds: A:P.64, A:Y.65, A:T.66, A:V.80, A:K.82, A:Y.84, A:F.85, A:K.97, A:M.98, A:S.99, A:S.99 Water bridges: A:T.88, A:G.95, A:T.156, A:T.156, A:Q.182 Salt bridges: A:R.63, A:R.63 pi-Stacking: A:Y.84, A:Y.84

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: R.17, I.19, A.34, L.35, P.38, G.75, F.76 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.75 GOL.3: 8 residues within 4Å: Chain A: G.151, G.152, A.180, N.181, D.211, F.223, P.247, M.250 5 PLIP interactions: 5 interactions with chain A Water bridges: A:N.181, A:N.181, A:D.211, A:D.211, A:G.222 GOL.4: 6 residues within 4Å: Chain A: F.92, A.94, G.95, G.96, K.97 Ligands: FAD.1 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.94, A:K.97 GOL.5: 7 residues within 4Å: Chain A: G.151, T.153, G.154, C.245, G.246, P.247 Ligands: FAD.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.151 Water bridges: A:T.153, A:G.246

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Takaba, K. et al., Distribution of valence electrons of the flavin cofactor in NADH-cytochrome b5 reductase. Sci Rep (2017)

Release Date

2017-04-05

Peptides

NADH-cytochrome b5 reductase 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NADH-cytochrome b5 reductase 3

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