SMTL ID : 3h1k.1

Chicken cytochrome BC1 complex with ZN++ and an iodinated derivative of kresoxim-methyl bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.48 Å

Oligo State

hetero-2-2-2-2-2-2-2-2-2-2-mer

Ligands

6 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)

PEE.1: 3 residues within 4Å: Chain A: Y.442 Chain C: H.222 Ligands: PEE.18 No protein-ligand interaction detected (PLIP) PEE.9: 20 residues within 4Å: Chain C: W.31, F.96, L.97, I.99, G.100, Y.104, Y.105, L.302, T.317, F.326, W.327, V.330, L.333, T.337, Y.359 Chain F: Y.29 Chain G: Q.44, V.48, F.52 Ligands: CDL.8 19 PLIP interactions: 17 interactions with chain C, 1 interactions with chain G, 1 interactions with chain F Hydrophobic interactions: C:W.31, C:W.31, C:F.96, C:L.97, C:I.99, C:Y.104, C:Y.104, C:Y.105, C:L.302, C:F.326, C:W.327, C:W.327, C:V.330, C:L.333, G:F.52 Hydrogen bonds: C:Y.104, C:Y.104, C:Y.105, F:Y.29 PEE.18: 15 residues within 4Å: Chain A: Y.442 Chain C: F.227, I.230 Chain D: K.226 Chain E: Y.37, T.40, C.44, T.47, K.52 Chain J: F.11, R.12, F.17, V.21, E.29 Ligands: PEE.1 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 3 interactions with chain J Salt bridges: D:K.226 Hydrophobic interactions: C:I.230, J:F.17, J:V.21 Hydrogen bonds: J:R.12 PEE.26: 16 residues within 4Å: Chain M: W.31, F.96, L.97, Y.104, Y.105, F.277, T.317, Q.323, F.326, W.327, L.333, Y.359 Chain P: Y.29 Chain Q: Q.44, V.48 Ligands: CDL.25 14 PLIP interactions: 13 interactions with chain M, 1 interactions with chain P Hydrophobic interactions: M:W.31, M:W.31, M:W.31, M:F.96, M:L.97, M:Y.104, M:Y.104, M:Y.105, M:F.277, M:W.327, M:L.333 Hydrogen bonds: M:Y.104, M:Y.105, P:Y.29 PEE.27: 3 residues within 4Å: Chain K: Y.442 Chain M: H.222 Ligands: PEE.36 2 PLIP interactions: 1 interactions with chain M, 1 interactions with chain K Salt bridges: M:H.222 Hydrogen bonds: K:Y.442 PEE.36: 15 residues within 4Å: Chain K: Y.442 Chain M: F.227, I.230 Chain O: Y.37, T.40, C.44, T.47, K.52 Chain T: F.11, R.12, T.14, F.17, A.18, E.29 Ligands: PEE.27 7 PLIP interactions: 1 interactions with chain N, 3 interactions with chain T, 2 interactions with chain M, 1 interactions with chain O Salt bridges: N:K.226 Hydrophobic interactions: T:F.17, T:A.18, M:I.230, M:I.230 Hydrogen bonds: T:R.12, O:T.40

5 x UNL: UNKNOWN LIGAND(Non-functional Binders)

UNL.2: 3 residues within 4Å: Chain A: Q.430, L.431, L.432 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.430 UNL.3: 2 residues within 4Å: Chain A: H.271, N.274 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.274 UNL.12: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.163 UNL.19: 1 residues within 4Å: Chain K: H.360 No protein-ligand interaction detected (PLIP) UNL.31: 2 residues within 4Å: Chain M: H.159, E.163 3 PLIP interactions: 3 interactions with chain M Hydrogen bonds: M:H.159, M:E.163, M:E.163

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

HEM.4: 22 residues within 4Å: Chain C: Q.45, I.46, G.49, L.50, L.52, A.53, Y.56, V.67, R.81, H.84, A.85, L.124, T.127, A.128, G.131, Y.132, L.134, P.135, H.183, F.184, P.187, I.190 20 PLIP interactions: 20 interactions with chain C, Hydrophobic interactions: C:Q.45, C:I.46, C:L.50, C:L.52, C:A.53, C:Y.56, C:V.67, C:L.124, C:T.127, C:L.134, C:L.134, C:F.184, C:I.190 Water bridges: C:A.85 Salt bridges: C:R.81, C:R.81 pi-Stacking: C:H.84, C:H.183 Metal complexes: C:H.84, C:H.183 HEM.5: 23 residues within 4Å: Chain C: W.32, G.35, S.36, L.38, A.39, I.95, H.98, I.99, R.101, S.107, T.113, W.114, G.117, V.118, L.120, L.121, T.194, H.197, L.198, L.201, S.206, N.207 Ligands: UQ.7 25 PLIP interactions: 25 interactions with chain C, Hydrophobic interactions: C:L.38, C:L.38, C:I.95, C:I.99, C:T.113, C:W.114, C:W.114, C:V.118, C:L.120, C:L.120, C:L.121, C:T.194, C:L.198, C:L.201 Hydrogen bonds: C:W.32, C:G.35, C:N.207 Water bridges: C:W.32, C:S.206 Salt bridges: C:H.98, C:R.101, C:R.101 pi-Stacking: C:H.98 Metal complexes: C:H.98, C:H.197 HEM.20: 22 residues within 4Å: Chain M: Q.45, I.46, G.49, L.50, L.52, A.53, Y.56, V.67, R.81, H.84, A.85, L.124, T.127, A.128, G.131, Y.132, L.134, P.135, H.183, F.184, P.187, I.190 20 PLIP interactions: 20 interactions with chain M, Hydrophobic interactions: M:Q.45, M:I.46, M:L.50, M:L.52, M:Y.56, M:V.67, M:A.85, M:L.124, M:T.127, M:A.128, M:L.134, M:L.134, M:F.184, M:P.187, M:I.190 Water bridges: M:A.85 Salt bridges: M:R.81, M:R.81 Metal complexes: M:H.84, M:H.183 HEM.21: 23 residues within 4Å: Chain M: W.32, G.35, S.36, L.38, A.39, I.95, H.98, I.99, R.101, S.107, T.113, W.114, G.117, V.118, L.120, L.121, T.194, H.197, L.198, L.201, S.206, N.207 Ligands: UQ.24 21 PLIP interactions: 21 interactions with chain M, Hydrophobic interactions: M:L.38, M:L.38, M:I.95, M:I.99, M:T.113, M:W.114, M:W.114, M:V.118, M:L.120, M:L.121, M:L.198, M:L.201 Hydrogen bonds: M:W.32, M:G.35, M:S.206, M:N.207 Salt bridges: M:H.98, M:R.101, M:R.101 Metal complexes: M:H.98, M:H.197

2 x IKR: methyl (2E)-{2-[(4-iodo-2,5-dimethylphenoxy)methyl]phenyl}(methoxyimino)ethanoate(Non-covalent)

IKR.6: 17 residues within 4Å: Chain C: M.125, F.129, Y.132, V.133, S.140, G.143, A.144, I.147, I.269, K.270, P.271, E.272, Y.274, F.275, A.278, Y.279, L.295 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:F.129, C:F.129, C:Y.132, C:I.269, C:P.271, C:F.275, C:F.275, C:A.278, C:Y.279, C:L.295 Hydrogen bonds: C:E.272 pi-Stacking: C:F.275 IKR.23: 16 residues within 4Å: Chain M: M.125, F.129, Y.132, V.133, S.140, G.143, A.144, I.147, I.269, K.270, P.271, E.272, Y.274, F.275, Y.279, L.295 12 PLIP interactions: 12 interactions with chain M Hydrophobic interactions: M:F.129, M:F.129, M:Y.132, M:I.147, M:I.269, M:P.271, M:F.275, M:F.275, M:Y.279, M:L.295 Hydrogen bonds: M:E.272 pi-Stacking: M:F.275

2 x UQ: Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer(Non-covalent)

UQ.7: 15 residues within 4Å: Chain C: S.18, L.19, L.22, P.23, A.24, I.28, S.36, A.39, L.198, L.201, H.202, S.206, F.221, D.229 Ligands: HEM.5 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.19, C:A.39, C:L.198, C:F.221 Hydrogen bonds: C:S.206 UQ.24: 15 residues within 4Å: Chain M: S.18, L.19, L.22, P.23, A.24, I.28, S.36, L.198, L.201, H.202, S.206, F.221, Y.225, D.229 Ligands: HEM.21 4 PLIP interactions: 4 interactions with chain M Hydrophobic interactions: M:L.19, M:L.198, M:F.221 Hydrogen bonds: M:S.206

4 x CDL: CARDIOLIPIN(Non-covalent)

CDL.8: 11 residues within 4Å: Chain C: S.29, A.30, W.31, Y.105 Chain F: H.72 Chain G: V.37, R.40, F.41, Q.44 Ligands: PEE.9, CDL.14 10 PLIP interactions: 5 interactions with chain C, 4 interactions with chain G, 1 interactions with chain F Hydrophobic interactions: C:W.31, G:V.37 Hydrogen bonds: C:S.29, C:A.30, C:Y.105, C:Y.105 Salt bridges: G:R.40, G:R.40, G:R.40, F:H.72 CDL.14: 12 residues within 4Å: Chain C: A.30, N.33, K.228, G.232, L.235 Chain D: Y.220, K.223, R.224 Chain F: H.72, R.73 Chain G: R.40 Ligands: CDL.8 10 PLIP interactions: 1 interactions with chain F, 2 interactions with chain G, 3 interactions with chain D, 4 interactions with chain C Salt bridges: F:R.73, G:R.40, D:K.223, D:K.231, C:K.228, C:K.228 Hydrogen bonds: G:R.40, D:R.224, C:N.33 Hydrophobic interactions: C:A.30 CDL.25: 11 residues within 4Å: Chain M: S.29, A.30, W.31, Y.105 Chain P: H.72 Chain Q: V.37, R.40, F.41, Q.44 Ligands: PEE.26, CDL.33 11 PLIP interactions: 5 interactions with chain M, 5 interactions with chain Q, 1 interactions with chain P Hydrophobic interactions: M:W.31, Q:V.37, Q:Q.44 Hydrogen bonds: M:S.29, M:A.30, M:Y.105, M:Y.105 Salt bridges: Q:R.40, Q:R.40, Q:R.40, P:H.72 CDL.33: 14 residues within 4Å: Chain M: A.30, N.33, K.228, G.232, L.235 Chain N: Y.220, K.223, R.224, K.231 Chain P: H.72, R.73 Chain Q: I.29, R.40 Ligands: CDL.25 13 PLIP interactions: 6 interactions with chain N, 5 interactions with chain M, 1 interactions with chain P, 1 interactions with chain Q Hydrophobic interactions: N:Y.220, N:Y.220, M:A.30, M:L.235 Hydrogen bonds: N:Y.220, M:N.33, Q:R.40 Salt bridges: N:K.223, N:R.224, N:K.231, M:K.228, M:K.228, P:R.73

2 x ZN: ZINC ION(Non-covalent)

ZN.10: 5 residues within 4Å: Chain C: D.253, P.254, E.255, H.268 Chain D: H.121 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Metal complexes: C:D.253, C:D.253, C:E.255, C:H.268, D:H.121 ZN.28: 5 residues within 4Å: Chain M: D.253, P.254, E.255, H.268 Chain N: H.121 4 PLIP interactions: 3 interactions with chain M, 1 interactions with chain N Metal complexes: M:D.253, M:E.255, M:H.268, N:H.121

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 7 residues within 4Å: Chain C: F.64, V.67, R.81, P.135, N.256, F.257 Chain D: Y.115 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:R.81, C:R.81, C:N.256, D:Y.115 GOL.30: 8 residues within 4Å: Chain M: F.64, V.67, A.68, C.71, R.81, N.256, F.257 Chain N: Y.115 3 PLIP interactions: 2 interactions with chain M, 1 interactions with chain N Hydrogen bonds: M:R.81, M:R.81, N:Y.115

2 x HEC: HEME C(Covalent)

HEC.13: 20 residues within 4Å: Chain D: V.32, V.36, C.37, A.39, C.40, H.41, N.105, A.108, P.110, P.111, R.120, Y.126, V.127, L.130, L.131, F.153, I.158, G.159, M.160, P.163 13 PLIP interactions: 13 interactions with chain D, Hydrophobic interactions: D:V.32, D:A.39, D:A.108, D:P.110, D:V.127, D:L.130, D:L.131, D:I.158, D:M.160, D:P.163 Hydrogen bonds: D:G.159 Salt bridges: D:R.120 Metal complexes: D:H.41 HEC.32: 22 residues within 4Å: Chain N: V.32, V.36, C.37, A.39, C.40, H.41, N.105, A.108, L.109, P.110, P.111, R.120, Y.126, V.127, L.130, L.131, F.153, I.158, G.159, M.160, P.163, V.186 16 PLIP interactions: 16 interactions with chain N, Hydrophobic interactions: N:V.32, N:A.39, N:A.108, N:P.110, N:V.127, N:L.130, N:L.131, N:I.158, N:M.160, N:P.163, N:V.186 Hydrogen bonds: N:Y.126, N:G.159 Salt bridges: N:R.120 pi-Stacking: N:H.41 Metal complexes: N:H.41

5 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.15: 12 residues within 4Å: Chain C: Y.76 Chain D: Q.200, R.203, M.204, K.207, M.208 Chain E: Y.49, A.50, N.53, Q.57 Chain J: D.37 Ligands: BOG.16 6 PLIP interactions: 2 interactions with chain D, 1 interactions with chain J, 1 interactions with chain C, 2 interactions with chain E Hydrogen bonds: D:Q.200, J:D.37, C:Y.76, E:N.53 Salt bridges: D:K.207 Hydrophobic interactions: E:Y.49 BOG.16: 3 residues within 4Å: Chain D: Q.200, R.203 Ligands: BOG.15 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.200, D:R.203, D:R.203 Salt bridges: D:R.203 BOG.22: 4 residues within 4Å: Chain M: M.14, L.198, T.199, H.202 3 PLIP interactions: 3 interactions with chain M Hydrogen bonds: M:L.198, M:L.198 Salt bridges: M:H.202 BOG.29: 3 residues within 4Å: Chain M: Y.76 Chain N: Q.200 Ligands: BOG.34 2 PLIP interactions: 1 interactions with chain N, 1 interactions with chain M Hydrogen bonds: N:Q.200, M:Y.76 BOG.34: 11 residues within 4Å: Chain M: Y.76 Chain N: Q.200, R.203, M.204, K.207, M.208 Chain O: Y.49, A.50, N.53, Q.57 Ligands: BOG.29 6 PLIP interactions: 3 interactions with chain O, 2 interactions with chain N, 1 interactions with chain T Hydrophobic interactions: O:Y.49 Hydrogen bonds: O:Y.49, O:N.53, N:Q.200, T:D.37 Salt bridges: N:K.207

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.17: 7 residues within 4Å: Chain E: C.139, H.141, L.142, C.144, C.158, H.161, S.163 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.139, E:H.141, E:C.158, E:H.161 FES.35: 8 residues within 4Å: Chain O: C.139, H.141, L.142, G.143, C.144, C.158, H.161, S.163 4 PLIP interactions: 4 interactions with chain O, Metal complexes: O:C.139, O:H.141, O:C.158, O:H.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Berry, E.A. et al., Crystallographic location of two Zn(2+)-binding sites in the avian cytochrome bc(1) complex. Biochim.Biophys.Acta (2000)

Release Date

2009-04-28

Peptides

MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN I: AK
MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 2: BL
Cytochrome b: CM
MITOCHONDRIAL CYTOCHROME C1, HEME PROTEIN: DN
Cytochrome b-c1 complex subunit Rieske, mitochondrial: EO
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 14 KDA PROTEIN: FP
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE UBIQUINONE-BINDING PROTEIN QP-C: GQ
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 11 KDA PROTEIN, COMPLEX III SUBUNIT VIII: HR
Cytochrome b-c1 complex subunit Rieske, mitochondrial: IS
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 7.2 KDA PROTEIN: JT

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

K
N

B
B

L
O

C
C

M
P

D
D

N
Q

E
E

O
R

F
F

P
S

G
G

Q
T

H
H

R
U

I
I

S
V

J
J

T
W

Membrane

We predict this structure to be a membrane protein.
Show / Hide

MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN I

MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 2

Cytochrome b

MITOCHONDRIAL CYTOCHROME C1, HEME PROTEIN

Cytochrome b-c1 complex subunit Rieske, mitochondrial

MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 14 KDA PROTEIN

MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE UBIQUINONE-BINDING PROTEIN QP-C

MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 11 KDA PROTEIN, COMPLEX III SUBUNIT VIII

Cytochrome b-c1 complex subunit Rieske, mitochondrial

MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 7.2 KDA PROTEIN

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