SMTL ID : 4o7g.1

Crystal Structure of Ascorbate-bound Cytochrome b561, crystal soaked in 1 M L-ascorbate for 40 minutes

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 25 residues within 4Å: Chain A: W.29, F.48, H.51, P.52, M.55, V.56, L.59, L.103, H.106, N.113, F.114, Y.115, S.116, H.118, S.119, G.122, L.123, A.168, T.171, A.172, G.175, I.176, E.178, K.179 Ligands: ASC.3 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:W.29, A:F.48, A:F.48, A:P.52, A:M.55, A:V.56, A:L.59, A:A.168, A:T.171, A:I.176, A:K.179 Hydrogen bonds: A:F.114, A:S.116, A:E.178 Water bridges: A:Y.115, A:S.119 Salt bridges: A:H.106, A:H.106 Metal complexes: A:H.51, A:H.118 HEM.2: 18 residues within 4Å: Chain A: M.67, Y.70, K.71, K.81, H.84, L.85, Q.88, F.129, Q.132, W.133, G.136, F.137, Y.140, M.154, H.157, V.158, G.161, V.217 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:K.81, A:L.85, A:L.85, A:Q.88, A:F.129, A:F.129, A:Q.132, A:W.133, A:V.158, A:V.217 Salt bridges: A:K.71 pi-Stacking: A:H.84 Metal complexes: A:H.84, A:H.157 HEM.5: 25 residues within 4Å: Chain B: F.48, H.51, P.52, M.55, V.56, L.59, A.102, L.103, H.106, N.113, F.114, S.116, H.118, S.119, G.122, L.123, C.125, T.171, A.172, G.175, I.176, E.178, K.179, F.182 Ligands: ASC.8 20 PLIP interactions: 20 interactions with chain B, Hydrophobic interactions: B:F.48, B:P.52, B:M.55, B:V.56, B:L.59, B:A.102, B:F.114, B:T.171 Hydrogen bonds: B:F.114, B:S.116, B:S.119, B:E.178 Water bridges: B:S.119, B:S.119 Salt bridges: B:H.106, B:H.106 pi-Stacking: B:H.51, B:H.118 Metal complexes: B:H.51, B:H.118 HEM.6: 22 residues within 4Å: Chain B: M.67, Y.70, K.71, K.77, K.81, H.84, L.85, Q.88, F.129, Q.132, W.133, G.136, F.137, Y.140, W.141, M.154, H.157, V.158, G.161, I.162, V.217 Ligands: ASC.7 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:Y.70, B:L.85, B:Q.88, B:F.129, B:Q.132, B:W.133, B:Y.140, B:Y.140, B:W.141, B:V.158, B:I.162 Salt bridges: B:K.71, B:K.77 Metal complexes: B:H.84, B:H.157

3 x ASC: ASCORBIC ACID(Non-covalent)

ASC.3: 8 residues within 4Å: Chain A: F.105, H.106, I.111, Y.115, F.182, N.186 Chain B: R.191 Ligands: HEM.1 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:H.106, A:N.186, B:R.191 Salt bridges: A:H.106, B:R.191 ASC.7: 7 residues within 4Å: Chain B: K.77, K.81, Y.140, R.150, A.151, M.154 Ligands: HEM.6 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.77, B:K.77, B:K.81, B:K.81 Salt bridges: B:K.77, B:K.81, B:R.150 ASC.8: 7 residues within 4Å: Chain B: F.105, H.106, I.111, Y.115, F.182, N.186 Ligands: HEM.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.106, B:Y.115 Salt bridges: B:H.106

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

SO4.4: 3 residues within 4Å: Chain A: K.81, Y.140, R.150 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.81, A:R.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lu, P. et al., Structure and mechanism of a eukaryotic transmembrane ascorbate-dependent oxidoreductase. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-02-05

Peptides

Probable transmembrane ascorbate ferrireductase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Probable transmembrane ascorbate ferrireductase 2

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