SMTL ID : 3ner.1

Structure of Human Type B Cytochrome b5

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.1: 19 residues within 4Å: Chain A: L.28, I.30, V.37, F.40, H.44, P.45, G.46, V.50, L.51, Q.54, S.62, F.63, V.66, H.68, S.69, A.72, M.75, L.76 Chain B: H.31 20 PLIP interactions: 19 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:L.28, A:I.30, A:V.37, A:F.40, A:F.40, A:P.45, A:V.50, A:L.51, A:Q.54, A:F.63, A:F.63, A:V.66, A:A.72, A:M.75, A:L.76 Hydrogen bonds: A:S.69 pi-Stacking: A:H.44 Metal complexes: A:H.44, A:H.68 Salt bridges: B:H.31 HEM.3: 16 residues within 4Å: Chain B: V.37, F.40, H.44, P.45, G.46, V.50, L.51, Q.54, S.62, F.63, V.66, H.68, S.69, A.72, M.75, L.76 24 PLIP interactions: 24 interactions with chain B, Hydrophobic interactions: B:V.37, B:F.40, B:F.40, B:P.45, B:P.45, B:V.50, B:V.50, B:L.51, B:Q.54, B:F.63, B:F.63, B:V.66, B:A.72, B:L.76 Hydrogen bonds: B:V.66, B:S.69 Water bridges: B:S.69, B:S.69, B:S.69 pi-Stacking: B:H.44, B:H.44, B:H.68 Metal complexes: B:H.44, B:H.68

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 1 residues within 4Å: Chain B: N.21 No protein-ligand interaction detected (PLIP)

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

SO4.4: 4 residues within 4Å: Chain A: D.65 Chain B: R.33, K.77, Y.80 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:D.65, B:K.77 Water bridges: B:R.33, B:R.33, B:R.33 Salt bridges: B:R.33, B:K.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Parthasarathy, S. et al., Accommodating a Non-Conservative Internal Mutation by Water-Mediated Hydrogen-Bonding Between beta-Sheet Strands: A Comparison of Human and Rat Type B (Mitochondrial) Cytochrome b5. Biochemistry (2011)

Release Date

2011-05-25

Peptides

Cytochrome b5 type B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cytochrome b5 type B