SMTL ID : 5zlg.1

Human duodenal cytochrome b (Dcytb) in zinc ion and ascorbate bound form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 25 residues within 4Å: Chain A: W.30, F.47, H.50, P.51, M.54, F.58, V.104, F.105, H.108, N.115, M.116, Y.117, S.118, H.120, S.121, G.124, V.128, V.170, T.173, A.174, G.177, L.178, E.180, K.181 Ligands: ASC.4 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:W.30, A:F.47, A:P.51, A:M.54, A:F.58, A:F.105, A:V.128, A:T.173, A:A.174, A:L.178, A:K.181 Hydrogen bonds: A:V.104, A:M.116, A:S.118, A:E.180 Salt bridges: A:H.108 Metal complexes: A:H.50, A:H.120 HEM.2: 23 residues within 4Å: Chain A: Q.62, I.66, Y.69, R.70, K.79, K.83, H.86, A.87, N.90, Y.131, Q.134, L.135, G.138, F.139, F.142, L.143, M.156, H.159, V.160, G.163, V.219, K.225 Ligands: ASC.5 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:I.66, A:Y.69, A:Y.69, A:K.83, A:A.87, A:N.90, A:Y.131, A:Y.131, A:Q.134, A:L.135, A:F.142, A:L.143, A:V.160, A:V.219 Salt bridges: A:R.70, A:K.79, A:K.225 pi-Stacking: A:H.86 Metal complexes: A:H.86, A:H.159 HEM.6: 25 residues within 4Å: Chain B: W.30, F.47, H.50, P.51, M.54, F.58, V.104, F.105, H.108, N.115, M.116, Y.117, S.118, H.120, S.121, G.124, V.128, V.170, T.173, A.174, G.177, L.178, E.180, K.181 Ligands: ASC.9 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:W.30, B:F.47, B:P.51, B:M.54, B:F.58, B:F.105, B:V.128, B:T.173, B:A.174, B:L.178, B:K.181 Hydrogen bonds: B:V.104, B:M.116, B:S.118, B:E.180 Salt bridges: B:H.108 Metal complexes: B:H.50, B:H.120 HEM.7: 23 residues within 4Å: Chain B: Q.62, I.66, Y.69, R.70, K.79, K.83, H.86, A.87, N.90, Y.131, Q.134, L.135, G.138, F.139, F.142, L.143, M.156, H.159, V.160, G.163, V.219, K.225 Ligands: ASC.10 20 PLIP interactions: 20 interactions with chain B, Hydrophobic interactions: B:I.66, B:Y.69, B:Y.69, B:K.83, B:A.87, B:N.90, B:Y.131, B:Y.131, B:Q.134, B:L.135, B:F.142, B:L.143, B:V.160, B:V.219 Salt bridges: B:R.70, B:K.79, B:K.225 pi-Stacking: B:H.86 Metal complexes: B:H.86, B:H.159

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: F.47, N.107, H.108 Ligands: ASC.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.108 ZN.8: 4 residues within 4Å: Chain B: F.47, N.107, H.108 Ligands: ASC.9 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.108

4 x ASC: ASCORBIC ACID(Non-covalent)

ASC.4: 6 residues within 4Å: Chain A: F.47, H.108, K.181, F.184 Ligands: HEM.1, ZN.3 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.181 ASC.5: 7 residues within 4Å: Chain A: K.79, K.83, F.142, R.152, A.153, M.156 Ligands: HEM.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.79, A:K.79, A:K.83, A:K.83, A:R.152 Salt bridges: A:K.83, A:R.152 ASC.9: 6 residues within 4Å: Chain B: F.47, H.108, K.181, F.184 Ligands: HEM.6, ZN.8 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.181 ASC.10: 7 residues within 4Å: Chain B: K.79, K.83, F.142, R.152, A.153, M.156 Ligands: HEM.7 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.79, B:K.79, B:K.83, B:K.83, B:R.152 Salt bridges: B:K.83, B:R.152

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ganasen, M. et al., Structural basis for promotion of duodenal iron absorption by enteric ferric reductase with ascorbate. Commun Biol (2018)

Release Date

2018-10-31

Peptides

Cytochrome b reductase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Membrane

We predict this structure to be a membrane protein.
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Cytochrome b reductase 1

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