SMTL ID : 5cic.1

Complex of yeast cytochrome c peroxidase (W191G) bound to 3-aminobenzotrifluoride with iso-1 cytochrome c

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-2-2-mer

Ligands

4 x HEC: HEME C(Non-covalent)

HEC.1: 24 residues within 4Å: Chain A: P.44, V.45, V.47, R.48, W.51, P.145, D.146, A.147, F.158, L.171, M.172, A.174, H.175, L.177, G.178, K.179, T.180, H.181, N.184, S.185, L.232, T.234, F.266 Ligands: 51R.2 25 PLIP interactions: 25 interactions with chain A, Hydrophobic interactions: A:R.48, A:W.51, A:W.51, A:W.51, A:P.145, A:F.158, A:L.171, A:A.174, A:L.177, A:T.180, A:L.232, A:F.266 Hydrogen bonds: A:K.179, A:H.181, A:N.184 Water bridges: A:D.37, A:D.37, A:D.37, A:V.45, A:R.48 Salt bridges: A:R.48, A:H.181, A:H.181 pi-Stacking: A:W.51 Metal complexes: A:H.175 HEC.3: 27 residues within 4Å: Chain A: A.194 Chain B: R.18, C.19, C.22, H.23, V.33, G.34, P.35, L.37, I.40, R.43, S.45, G.46, Y.51, Y.53, T.54, N.57, W.64, M.69, Y.72, L.73, T.83, K.84, M.85, A.86, F.87, L.99 25 PLIP interactions: 24 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:V.33, B:P.35, B:L.37, B:L.37, B:I.40, B:I.40, B:W.64, B:L.73, B:L.73, B:M.85, B:F.87, B:L.99, B:L.99, A:A.194 Hydrogen bonds: B:G.46, B:Y.53, B:T.54, B:N.57, B:T.83, B:K.84 Water bridges: B:T.83 Salt bridges: B:R.43, B:K.84 pi-Stacking: B:Y.72 Metal complexes: B:H.23 HEC.4: 23 residues within 4Å: Chain C: P.44, V.45, V.47, R.48, W.51, P.145, D.146, A.147, L.171, M.172, A.174, H.175, L.177, G.178, K.179, T.180, H.181, N.184, S.185, L.232, T.234, F.266 Ligands: 51R.5 25 PLIP interactions: 25 interactions with chain C, Hydrophobic interactions: C:P.44, C:V.47, C:R.48, C:W.51, C:W.51, C:W.51, C:P.145, C:P.145, C:A.147, C:L.171, C:A.174, C:L.177, C:T.180, C:F.266 Hydrogen bonds: C:K.179, C:H.181, C:N.184, C:S.185 Water bridges: C:R.48, C:R.48 Salt bridges: C:R.48, C:H.181, C:H.181 pi-Stacking: C:W.51 Metal complexes: C:H.175 HEC.6: 28 residues within 4Å: Chain C: A.193, A.194 Chain D: R.18, C.19, Q.21, C.22, H.23, V.33, G.34, P.35, L.37, I.40, S.45, G.46, Y.51, Y.53, T.54, N.57, W.64, M.69, Y.72, L.73, T.83, K.84, M.85, A.86, F.87, L.99 20 PLIP interactions: 20 interactions with chain D, Hydrophobic interactions: D:L.37, D:L.37, D:I.40, D:I.40, D:L.73, D:K.84, D:M.85, D:F.87, D:F.87, D:L.99, D:L.99 Hydrogen bonds: D:G.46, D:T.54, D:N.57, D:T.83, D:T.83, D:K.84 Salt bridges: D:K.84 pi-Stacking: D:Y.72 Metal complexes: D:H.23

2 x 51R: 3-(trifluoromethyl)aniline(Non-covalent)

51R.2: 11 residues within 4Å: Chain A: H.175, A.176, L.177, G.178, T.180, G.189, P.190, G.191, M.230, L.232 Ligands: HEC.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.180 pi-Stacking: A:H.175 Halogen bonds: A:G.189 51R.5: 12 residues within 4Å: Chain C: H.175, L.177, G.178, K.179, T.180, G.191, F.202, M.230, M.231, L.232, D.235 Ligands: HEC.4 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:H.175, C:T.180 Hydrogen bonds: C:H.175 Halogen bonds: C:D.235

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Payne, T.M. et al., Constraints on the Radical Cation Center of Cytochrome c Peroxidase for Electron Transfer from Cytochrome c. Biochemistry (2016)

Release Date

2016-08-03

Peptides

Cytochrome c peroxidase, mitochondrial: AC
Cytochrome c iso-1: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Cytochrome c peroxidase, mitochondrial

Cytochrome c iso-1

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