SMTL ID : 7tay.1

Bos Taurus Mitochondrial BC1 in complex with Pyramoxadone

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

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

Ligands

4 x 6PE: 1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE(Non-covalent)

6PE.1: 10 residues within 4Å: Chain A: S.439, G.440, F.442, W.443, L.444 Chain C: H.221, T.225, I.229 Ligands: CDL.2, PX4.13 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Salt bridges: C:H.221, C:H.221 Hydrogen bonds: A:S.439, A:S.439 6PE.14: 9 residues within 4Å: Chain K: L.32, T.36, W.38, R.39, L.40 Chain N: Y.155, I.156, N.159, L.160 7 PLIP interactions: 3 interactions with chain K, 4 interactions with chain N Hydrophobic interactions: K:T.36, N:I.156 Hydrogen bonds: K:R.39, K:L.40, N:Y.155, N:Y.155, N:N.159 6PE.15: 10 residues within 4Å: Chain L: S.439, G.440, F.442, W.443, L.444 Chain N: H.221, T.225, I.229 Ligands: CDL.16, PX4.27 4 PLIP interactions: 2 interactions with chain N, 2 interactions with chain L Salt bridges: N:H.221, N:H.221 Hydrogen bonds: L:S.439, L:S.439 6PE.28: 9 residues within 4Å: Chain C: Y.155, I.156, N.159, L.160 Chain V: L.32, T.36, W.38, R.39, L.40 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain V Hydrophobic interactions: C:I.156, V:T.36 Hydrogen bonds: C:Y.155, C:Y.155, C:N.159, V:R.39, V:L.40

6 x CDL: CARDIOLIPIN(Non-covalent)

CDL.2: 15 residues within 4Å: Chain A: F.336, F.442, W.443, L.444, R.445 Chain C: N.3, I.4, R.5, F.18, I.19, H.221, T.225 Chain K: W.24 Ligands: 6PE.1, PX4.13 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:F.18, C:I.19, C:T.225, A:L.444 Salt bridges: C:R.5, A:R.445 Hydrogen bonds: A:L.444, A:R.445, A:R.445 CDL.8: 14 residues within 4Å: Chain C: S.28, S.29, W.30, F.33, Y.104, L.234, A.238 Chain F: Q.72 Chain G: V.37, R.40, T.41, C.44 Ligands: 8PE.6, CDL.11 8 PLIP interactions: 1 interactions with chain F, 4 interactions with chain C, 3 interactions with chain G Hydrogen bonds: F:Q.72, C:S.28, C:S.28, C:S.29, C:S.29 Salt bridges: G:R.40, G:R.40, G:R.40 CDL.11: 27 residues within 4Å: Chain C: S.29, N.32, F.33, L.36, M.89, K.227, L.230, G.231, L.234, L.235, A.238 Chain D: L.216, P.217, Y.220, K.223, R.224, K.231 Chain F: R.71, Q.72 Chain G: Y.29, F.30, G.33, I.34, N.36, V.37, R.40 Ligands: CDL.8 12 PLIP interactions: 7 interactions with chain D, 2 interactions with chain G, 3 interactions with chain C Hydrogen bonds: D:Y.220, D:Y.220, D:R.224, D:K.231, G:R.40 Salt bridges: D:K.223, D:R.224, D:K.231, C:K.227 Hydrophobic interactions: G:F.30, C:N.32, C:L.36 CDL.16: 15 residues within 4Å: Chain L: F.336, F.442, W.443, L.444, R.445 Chain N: N.3, I.4, R.5, F.18, I.19, H.221, T.225 Chain V: W.24 Ligands: 6PE.15, PX4.27 9 PLIP interactions: 4 interactions with chain N, 5 interactions with chain L Hydrophobic interactions: N:F.18, N:I.19, N:T.225, L:L.444 Salt bridges: N:R.5, L:R.445 Hydrogen bonds: L:L.444, L:R.445, L:R.445 CDL.22: 14 residues within 4Å: Chain N: S.28, S.29, W.30, F.33, Y.104, L.234, A.238 Chain Q: Q.72 Chain R: V.37, R.40, T.41, C.44 Ligands: 8PE.20, CDL.25 8 PLIP interactions: 3 interactions with chain R, 1 interactions with chain Q, 4 interactions with chain N Salt bridges: R:R.40, R:R.40, R:R.40 Hydrogen bonds: Q:Q.72, N:S.28, N:S.28, N:S.29, N:S.29 CDL.25: 27 residues within 4Å: Chain N: S.29, N.32, F.33, L.36, M.89, K.227, L.230, G.231, L.234, L.235, A.238 Chain O: L.216, P.217, Y.220, K.223, R.224, K.231 Chain Q: R.71, Q.72 Chain R: Y.29, F.30, G.33, I.34, N.36, V.37, R.40 Ligands: CDL.22 12 PLIP interactions: 3 interactions with chain N, 7 interactions with chain O, 2 interactions with chain R Hydrophobic interactions: N:N.32, N:L.36, R:F.30 Salt bridges: N:K.227, O:K.223, O:R.224, O:K.231 Hydrogen bonds: O:Y.220, O:Y.220, O:R.224, O:K.231, R:R.40

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

HEM.3: 30 residues within 4Å: Chain C: L.41, Q.44, I.45, G.48, L.49, L.51, A.52, Y.55, V.66, R.80, H.83, A.84, A.87, F.90, V.123, T.126, A.127, G.130, Y.131, L.133, P.134, F.179, H.182, F.183, P.186, F.187, I.189, N.255, Y.273 Ligands: PQU.5 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:L.41, C:Q.44, C:L.51, C:Y.55, C:F.90, C:T.126, C:L.133, C:L.133, C:F.183 Salt bridges: C:R.80, C:R.80 pi-Stacking: C:H.83, C:H.83, C:H.83, C:H.182, C:H.182 Metal complexes: C:H.83, C:H.182 HEM.4: 30 residues within 4Å: Chain C: W.31, G.34, S.35, L.37, G.38, L.41, F.90, L.94, H.97, V.98, R.100, G.101, S.106, Y.107, F.109, T.112, W.113, G.116, V.117, L.119, L.120, V.123, I.189, A.193, H.196, L.197, L.200, S.205, N.206, L.301 19 PLIP interactions: 19 interactions with chain C, Hydrophobic interactions: C:L.37, C:L.37, C:L.94, C:V.117, C:L.119, C:L.119, C:L.120, C:L.200, C:L.200 Hydrogen bonds: C:W.31, C:G.34, C:S.106, C:N.206 Salt bridges: C:H.97, C:R.100, C:R.100 pi-Cation interactions: C:R.100 Metal complexes: C:H.97, C:H.196 HEM.17: 30 residues within 4Å: Chain N: L.41, Q.44, I.45, G.48, L.49, L.51, A.52, Y.55, V.66, R.80, H.83, A.84, A.87, F.90, V.123, T.126, A.127, G.130, Y.131, L.133, P.134, F.179, H.182, F.183, P.186, F.187, I.189, N.255, Y.273 Ligands: PQU.19 18 PLIP interactions: 18 interactions with chain N, Hydrophobic interactions: N:L.41, N:Q.44, N:L.51, N:Y.55, N:F.90, N:T.126, N:L.133, N:L.133, N:F.183 Salt bridges: N:R.80, N:R.80 pi-Stacking: N:H.83, N:H.83, N:H.83, N:H.182, N:H.182 Metal complexes: N:H.83, N:H.182 HEM.18: 30 residues within 4Å: Chain N: W.31, G.34, S.35, L.37, G.38, L.41, F.90, L.94, H.97, V.98, R.100, G.101, S.106, Y.107, F.109, T.112, W.113, G.116, V.117, L.119, L.120, V.123, I.189, A.193, H.196, L.197, L.200, S.205, N.206, L.301 19 PLIP interactions: 19 interactions with chain N, Hydrophobic interactions: N:L.37, N:L.37, N:L.94, N:V.117, N:L.119, N:L.119, N:L.120, N:L.200, N:L.200 Hydrogen bonds: N:W.31, N:G.34, N:S.106, N:N.206 Salt bridges: N:H.97, N:R.100, N:R.100 pi-Cation interactions: N:R.100 Metal complexes: N:H.97, N:H.196

2 x PQU: (5S)-3-anilino-5-methyl-5-(6-phenoxypyridin-3-yl)-1,3-oxazolidine-2,4-dione(Non-covalent)

PQU.5: 22 residues within 4Å: Chain C: F.91, Y.95, M.124, A.127, F.128, Y.131, M.138, W.141, G.142, V.145, I.146, I.268, P.270, E.271, Y.273, F.274, F.276, A.277, Y.278, L.294, I.298 Ligands: HEM.3 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:F.128, C:Y.131, C:V.145, C:I.146, C:I.268, C:P.270, C:P.270, C:E.271, C:Y.273, C:F.274, C:F.274, C:F.276, C:A.277, C:I.298 Hydrogen bonds: C:E.271 pi-Stacking: C:F.274 PQU.19: 22 residues within 4Å: Chain N: F.91, Y.95, M.124, A.127, F.128, Y.131, M.138, W.141, G.142, V.145, I.146, I.268, P.270, E.271, Y.273, F.274, F.276, A.277, Y.278, L.294, I.298 Ligands: HEM.17 16 PLIP interactions: 16 interactions with chain N Hydrophobic interactions: N:F.128, N:Y.131, N:V.145, N:I.146, N:I.268, N:P.270, N:P.270, N:E.271, N:Y.273, N:F.274, N:F.274, N:F.276, N:A.277, N:I.298 Hydrogen bonds: N:E.271 pi-Stacking: N:F.274

2 x 8PE: (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate(Non-covalent)

8PE.6: 28 residues within 4Å: Chain C: W.30, Y.95, M.96, V.98, G.99, R.100, L.102, Y.103, Y.104, P.208, W.272, F.276, L.301, M.316, Q.322, F.325, W.326, V.329, L.332, L.333, T.336 Chain F: Q.72 Chain G: R.39, R.40, C.44, V.48, F.52 Ligands: CDL.8 21 PLIP interactions: 1 interactions with chain F, 19 interactions with chain C, 1 interactions with chain G Hydrogen bonds: F:Q.72, C:W.30, C:Y.103, C:Y.103, C:Y.104 Hydrophobic interactions: C:W.30, C:W.30, C:Y.95, C:Y.95, C:Y.95, C:Y.103, C:Y.103, C:Y.104, C:F.276, C:F.276, C:F.325, C:W.326, C:W.326, C:V.329, C:L.332, G:F.52 8PE.20: 28 residues within 4Å: Chain N: W.30, Y.95, M.96, V.98, G.99, R.100, L.102, Y.103, Y.104, P.208, W.272, F.276, L.301, M.316, Q.322, F.325, W.326, V.329, L.332, L.333, T.336 Chain Q: Q.72 Chain R: R.39, R.40, C.44, V.48, F.52 Ligands: CDL.22 21 PLIP interactions: 19 interactions with chain N, 1 interactions with chain R, 1 interactions with chain Q Hydrophobic interactions: N:W.30, N:W.30, N:Y.95, N:Y.95, N:Y.95, N:Y.103, N:Y.103, N:Y.104, N:F.276, N:F.276, N:F.325, N:W.326, N:W.326, N:V.329, N:L.332, R:F.52 Hydrogen bonds: N:W.30, N:Y.103, N:Y.103, N:Y.104, Q:Q.72

2 x PEF: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PEF.7: 28 residues within 4Å: Chain C: L.43, L.46, F.50, Y.75, I.78, M.82, L.233, I.236, M.240 Chain D: H.200, R.203, M.204, K.207, M.208, M.211, M.212, L.215 Chain J: D.36 Chain P: V.47, Y.49, A.50, A.51, N.53, V.54, V.55, Q.57, F.58 Ligands: PX4.13 17 PLIP interactions: 1 interactions with chain J, 3 interactions with chain C, 9 interactions with chain P, 4 interactions with chain D Hydrogen bonds: J:D.36, P:N.53, P:Q.57 Hydrophobic interactions: C:L.46, C:I.236, C:I.236, P:Y.49, P:A.50, P:A.51, P:V.54, P:V.54, P:F.58, P:F.58, D:M.211, D:L.215 Salt bridges: D:H.200, D:K.207 PEF.21: 28 residues within 4Å: Chain E: V.47, Y.49, A.50, A.51, N.53, V.54, V.55, Q.57, F.58 Chain N: L.43, L.46, F.50, Y.75, I.78, M.82, L.233, I.236, M.240 Chain O: H.200, R.203, M.204, K.207, M.208, M.211, M.212, L.215 Chain U: D.36 Ligands: PX4.27 17 PLIP interactions: 9 interactions with chain E, 3 interactions with chain N, 1 interactions with chain U, 4 interactions with chain O Hydrophobic interactions: E:Y.49, E:A.50, E:A.51, E:V.54, E:V.54, E:F.58, E:F.58, N:L.46, N:I.236, N:I.236, O:M.211, O:L.215 Hydrogen bonds: E:N.53, E:Q.57, U:D.36 Salt bridges: O:H.200, O:K.207

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 4 residues within 4Å: Chain C: F.63, V.66, T.67, Y.256 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain N: F.63, V.66, T.67, Y.256 Ligand excluded by PLIP

2 x HEC: HEME C(Covalent)

HEC.10: 26 residues within 4Å: Chain D: V.32, V.36, C.37, S.39, C.40, H.41, N.105, A.108, L.109, P.110, P.111, L.113, I.116, R.120, Y.126, V.127, L.130, L.131, F.153, I.158, G.159, M.160, P.163, I.164, V.186, L.190 19 PLIP interactions: 19 interactions with chain D, Hydrophobic interactions: D:V.32, D:N.105, D:A.108, D:P.110, D:P.111, D:I.116, D:L.130, D:L.131, D:L.131, D:F.153, D:I.158, D:M.160, D:P.163, D:I.164 Hydrogen bonds: D:Y.126, D:Y.126, D:G.159 Salt bridges: D:R.120 Metal complexes: D:H.41 HEC.24: 26 residues within 4Å: Chain O: V.32, V.36, C.37, S.39, C.40, H.41, N.105, A.108, L.109, P.110, P.111, L.113, I.116, R.120, Y.126, V.127, L.130, L.131, F.153, I.158, G.159, M.160, P.163, I.164, V.186, L.190 19 PLIP interactions: 19 interactions with chain O, Hydrophobic interactions: O:V.32, O:N.105, O:A.108, O:P.110, O:P.111, O:I.116, O:L.130, O:L.131, O:L.131, O:F.153, O:I.158, O:M.160, O:P.163, O:I.164 Hydrogen bonds: O:Y.126, O:Y.126, O:G.159 Salt bridges: O:R.120 Metal complexes: O:H.41

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

FES.12: 10 residues within 4Å: Chain E: C.139, H.141, L.142, C.144, C.158, C.160, H.161, G.162, S.163, P.175 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.139, E:H.141, E:C.158, E:H.161 FES.26: 10 residues within 4Å: Chain P: C.139, H.141, L.142, C.144, C.158, C.160, H.161, G.162, S.163, P.175 4 PLIP interactions: 4 interactions with chain P, Metal complexes: P:C.139, P:H.141, P:C.158, P:H.161

2 x PX4: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PX4.13: 36 residues within 4Å: Chain A: Y.416, D.417, F.442, L.444 Chain C: I.39, I.229, A.232, L.233, I.236 Chain D: M.222, K.226 Chain J: Y.10, F.14, R.15, R.16, T.17, F.20, A.21, I.24, V.25 Chain K: W.24, V.27, G.28, G.31, L.32, W.34, A.35 Chain P: Y.37, T.40, T.43, T.44, V.47, A.48 Ligands: 6PE.1, CDL.2, PEF.7 13 PLIP interactions: 5 interactions with chain J, 3 interactions with chain C, 2 interactions with chain A, 3 interactions with chain P Hydrophobic interactions: J:A.21, J:I.24, J:I.24, J:V.25, C:I.229, C:A.232, C:I.236, P:T.44 pi-Cation interactions: J:F.20, A:F.442, P:Y.37 Salt bridges: A:D.417 Hydrogen bonds: P:T.40 PX4.27: 36 residues within 4Å: Chain E: Y.37, T.40, T.43, T.44, V.47, A.48 Chain L: Y.416, D.417, F.442, L.444 Chain N: I.39, I.229, A.232, L.233, I.236 Chain O: M.222, K.226 Chain U: Y.10, F.14, R.15, R.16, T.17, F.20, A.21, I.24, V.25 Chain V: W.24, V.27, G.28, G.31, L.32, W.34, A.35 Ligands: 6PE.15, CDL.16, PEF.21 13 PLIP interactions: 3 interactions with chain N, 3 interactions with chain E, 2 interactions with chain L, 5 interactions with chain U Hydrophobic interactions: N:I.229, N:A.232, N:I.236, E:T.44, U:A.21, U:I.24, U:I.24, U:V.25 Hydrogen bonds: E:T.40 pi-Cation interactions: E:Y.37, L:F.442, U:F.20 Salt bridges: L:D.417

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xia, D. et al., Conformation Switch of Rieske ISP subunit is revealed by the Crystal Structure of Bacterial Cytochrome bc1 in Complex with Azoxystrobin. to be published

Release Date

2023-01-18

Peptides

Cytochrome b-c1 complex subunit 1, mitochondrial: AL
Cytochrome b-c1 complex subunit 2, mitochondrial: BM
Cytochrome b: CN
Cytochrome c1, heme protein, mitochondrial: DO
Cytochrome b-c1 complex subunit Rieske, mitochondrial: EP
Cytochrome b-c1 complex subunit 7: FQ
Cytochrome b-c1 complex subunit 8: GR
Cytochrome b-c1 complex subunit 6, mitochondrial: HS
Cytochrome b-c1 complex subunit Rieske, mitochondrial: IT
Cytochrome b-c1 complex subunit 9: JU
Cytochrome b-c1 complex subunit 10: KV

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

L
A

B
B

M
B

C
C

N
C

D
D

O
D

E
E

P
E

F
F

Q
F

G
G

R
G

H
H

S
H

I
I

T
I

J
J

U
J

K
K

V
K

Membrane

We predict this structure to be a membrane protein.
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Cytochrome b-c1 complex subunit 1, mitochondrial

Cytochrome b-c1 complex subunit 2, mitochondrial

Cytochrome b

Cytochrome c1, heme protein, mitochondrial

Cytochrome b-c1 complex subunit Rieske, mitochondrial

Cytochrome b-c1 complex subunit 7

Cytochrome b-c1 complex subunit 8

Cytochrome b-c1 complex subunit 6, mitochondrial

Cytochrome b-c1 complex subunit Rieske, mitochondrial

Cytochrome b-c1 complex subunit 9

Cytochrome b-c1 complex subunit 10

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