SMTL ID : 7jrp.1

Plant Mitochondrial complex SC III2+IV from Vigna radiata

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-2-2-2-2-2-2-1-1-1-1-1-1-1-1-1-1-mer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: H.137, H.141, E.217 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.137, A:H.141, A:E.217, A:E.217 ZN.17: 3 residues within 4Å: Chain K: H.137, H.141, E.217 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:H.137, K:H.141, K:E.217, K:E.217 ZN.54: 5 residues within 4Å: Chain Y: C.101, G.103, H.110, C.125, C.128 4 PLIP interactions: 4 interactions with chain Y Metal complexes: Y:C.101, Y:H.110, Y:C.125, Y:C.128

5 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.2: 12 residues within 4Å: Chain A: Y.497, Y.523, N.525 Chain E: Y.112, R.119 Chain I: M.21, N.24, Y.27, V.28 Chain J: L.32 Ligands: CDL.3, CDL.4 8 PLIP interactions: 2 interactions with chain I, 3 interactions with chain A, 2 interactions with chain E, 1 interactions with chain J Hydrogen bonds: I:N.24, A:N.525 pi-Cation interactions: I:Y.27, A:Y.523, E:Y.112 Salt bridges: A:D.498, E:R.119 Hydrophobic interactions: J:L.32 PC1.19: 10 residues within 4Å: Chain K: Y.497, D.498, Y.523, N.525 Chain O: Y.112, R.119 Chain S: Y.27, V.31 Ligands: CDL.18, CDL.21 9 PLIP interactions: 4 interactions with chain K, 3 interactions with chain O, 2 interactions with chain S Hydrogen bonds: K:Y.523, K:N.525 Salt bridges: K:D.498, O:R.119, O:R.119 pi-Cation interactions: K:Y.523, O:Y.112, S:Y.27 Hydrophobic interactions: S:V.31 PC1.30: 9 residues within 4Å: Chain N: L.282, Y.286 Chain O: F.110, V.114, G.118 Chain Q: K.21, V.22, M.23, T.24 5 PLIP interactions: 3 interactions with chain Q, 1 interactions with chain O, 1 interactions with chain N Hydrogen bonds: Q:V.22, Q:M.23, Q:T.24 Hydrophobic interactions: O:V.114, N:L.282 PC1.36: 11 residues within 4Å: Chain 2: K.34, S.37, V.38, L.42 Chain U: M.1, F.9 Chain W: P.16, I.19, L.23 Ligands: PC1.56, 3PE.58 4 PLIP interactions: 2 interactions with chain W, 1 interactions with chain 2, 1 interactions with chain U Hydrophobic interactions: W:I.19, W:L.23, 2:L.42, U:F.9 PC1.56: 14 residues within 4Å: Chain 2: G.53, Y.57, S.60, H.61 Chain 3: Y.84, F.88 Chain U: W.106, P.110, L.112, L.113, L.120 Chain W: S.22 Ligands: PC1.36, 3PE.58 7 PLIP interactions: 5 interactions with chain U, 2 interactions with chain 2 Hydrophobic interactions: U:W.106, U:P.110, U:L.112, U:L.113, U:L.113 Hydrogen bonds: 2:S.60, 2:S.60

9 x CDL: CARDIOLIPIN(Non-covalent)

CDL.3: 16 residues within 4Å: Chain A: Y.417, Q.421, R.520, R.521, W.524, N.525, R.526 Chain C: S.9, L.10, L.11, I.24, F.227, Y.228 Chain J: W.21 Ligands: PC1.2, CDL.4 14 PLIP interactions: 9 interactions with chain A, 4 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: A:N.525, C:I.24, C:Y.228, C:Y.228, J:W.21 Hydrogen bonds: A:Y.523, A:N.525, A:R.526, C:S.9 Salt bridges: A:R.520, A:R.521, A:R.521, A:R.526, A:R.526 CDL.4: 14 residues within 4Å: Chain A: R.520, N.525 Chain C: I.48, Y.228, Y.232, L.236, A.243 Chain D: Y.287 Chain E: R.119, Y.122, A.123, I.126 Ligands: PC1.2, CDL.3 13 PLIP interactions: 2 interactions with chain D, 5 interactions with chain E, 4 interactions with chain C, 2 interactions with chain A Hydrogen bonds: D:Y.287, D:Y.287, E:R.119, C:Y.228, A:N.525 Hydrophobic interactions: E:Y.122, E:A.123, E:I.126, C:I.48, C:Y.232, C:A.243 Salt bridges: E:R.119, A:R.520 CDL.12: 15 residues within 4Å: Chain C: S.33, Y.34, W.35, F.38, Y.109, A.241, F.242 Chain F: H.76 Chain G: K.37, E.40, N.41, W.42, A.45 Ligands: 3PE.11, CDL.14 11 PLIP interactions: 1 interactions with chain F, 6 interactions with chain G, 4 interactions with chain C Salt bridges: F:H.76, G:K.37 Hydrophobic interactions: G:N.41, G:W.42, G:A.45, C:W.35, C:W.35, C:A.241 Hydrogen bonds: G:E.40, G:N.41, C:Y.34 CDL.14: 10 residues within 4Å: Chain C: Y.34 Chain D: L.281, L.282, A.285, R.288, R.289 Chain G: L.26, L.30, K.37 Ligands: CDL.12 6 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C, 2 interactions with chain G Hydrophobic interactions: D:L.281 Hydrogen bonds: D:R.289, C:Y.34 Salt bridges: D:R.288, G:K.37, G:K.37 CDL.18: 15 residues within 4Å: Chain K: Y.417, Q.421, R.520, R.521, W.524, N.525, R.526 Chain M: S.9, L.11, I.24, Y.228, W.239 Chain T: W.21 Ligands: PC1.19, CDL.21 11 PLIP interactions: 5 interactions with chain M, 5 interactions with chain K, 1 interactions with chain T Hydrophobic interactions: M:L.11, M:Y.228, M:W.239, T:W.21 Hydrogen bonds: M:S.9, M:S.9, K:N.525, K:R.526 Salt bridges: K:R.520, K:R.521, K:R.526 CDL.21: 18 residues within 4Å: Chain K: R.520, N.525 Chain M: I.48, Y.228, Y.232, L.236, W.239, A.243, F.246, F.251 Chain N: Y.287 Chain O: R.119, Y.122, L.125, I.126, L.128 Ligands: CDL.18, PC1.19 18 PLIP interactions: 9 interactions with chain M, 2 interactions with chain K, 2 interactions with chain N, 5 interactions with chain O Hydrophobic interactions: M:I.48, M:L.236, M:W.239, M:A.243, M:F.246, M:F.251, M:F.251, O:Y.122, O:L.125, O:I.126, O:L.128 Hydrogen bonds: M:Y.228, M:Y.232, K:N.525, N:Y.287, N:Y.287 Salt bridges: K:R.520, O:R.119 CDL.29: 12 residues within 4Å: Chain M: Y.34, F.38, F.242 Chain N: A.285, R.288, R.289 Chain Q: L.26, L.30, K.33, I.34, K.37 Ligands: CDL.31 9 PLIP interactions: 1 interactions with chain P, 3 interactions with chain M, 3 interactions with chain Q, 2 interactions with chain N Salt bridges: P:H.76, Q:K.33, Q:K.37, Q:K.37, N:R.288, N:R.289 Hydrophobic interactions: M:Y.34, M:F.38, M:F.38 CDL.31: 11 residues within 4Å: Chain M: S.33, Y.34, W.35, F.38 Chain P: H.76 Chain Q: K.37, V.38, N.41, A.45 Ligands: 3PE.25, CDL.29 9 PLIP interactions: 1 interactions with chain P, 4 interactions with chain M, 4 interactions with chain Q Salt bridges: P:H.76, M:K.234, Q:K.37 Hydrophobic interactions: M:W.35, M:F.38, Q:V.38, Q:N.41, Q:A.45 Hydrogen bonds: M:Y.34 CDL.39: 14 residues within 4Å: Chain 3: Y.55, M.60, K.66, M.67, A.70, V.71 Chain U: R.6, W.7, L.8, L.19, I.22, F.403, V.474 Ligands: 3PE.58 11 PLIP interactions: 7 interactions with chain U, 4 interactions with chain 3 Hydrophobic interactions: U:L.8, U:L.19, U:I.22, U:I.22, U:F.403, U:V.474, 3:A.70, 3:V.71 Hydrogen bonds: U:R.6, 3:Y.55 Salt bridges: 3:K.66

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

HEM.5: 20 residues within 4Å: Chain C: L.46, Q.49, I.50, G.53, V.54, L.56, Y.60, R.85, H.88, A.92, A.134, G.137, Y.138, L.140, P.141, H.189, Y.190, P.193, F.194, Y.280 15 PLIP interactions: 15 interactions with chain C, Hydrophobic interactions: C:L.46, C:Q.49, C:L.56, C:Y.60, C:L.140, C:L.140, C:Y.190, C:P.193, C:F.194 Salt bridges: C:R.85, C:R.85 pi-Stacking: C:H.88, C:H.189 Metal complexes: C:H.88, C:H.189 HEM.6: 21 residues within 4Å: Chain C: W.36, G.39, A.42, G.43, F.95, V.99, H.102, I.103, R.105, S.111, V.119, W.120, G.123, V.124, I.126, S.200, H.203, L.204, L.207, S.212, N.213 22 PLIP interactions: 22 interactions with chain C, Hydrophobic interactions: C:A.42, C:F.95, C:V.99, C:I.103, C:V.119, C:W.120, C:V.124, C:I.126, C:L.207 Hydrogen bonds: C:W.36, C:G.39, C:S.111, C:S.212, C:S.212, C:N.213 Salt bridges: C:H.102, C:R.105, C:R.105, C:R.116 pi-Cation interactions: C:R.105 Metal complexes: C:H.102, C:H.203 HEM.22: 22 residues within 4Å: Chain M: Q.49, I.50, G.53, V.54, L.56, A.57, Y.60, V.71, R.85, H.88, A.89, A.92, F.95, A.134, G.137, Y.138, L.140, P.141, H.189, Y.190, P.193, Y.280 12 PLIP interactions: 12 interactions with chain M, Hydrophobic interactions: M:Q.49, M:L.56, M:Y.60, M:A.89, M:F.95, M:L.140, M:Y.190, M:P.193 Salt bridges: M:R.85, M:R.85 Metal complexes: M:H.88, M:H.189 HEM.23: 19 residues within 4Å: Chain M: W.36, G.39, G.43, F.95, V.99, H.102, I.103, R.105, S.111, W.120, G.123, V.124, I.126, S.200, H.203, L.204, L.207, S.212, N.213 18 PLIP interactions: 18 interactions with chain M, Hydrophobic interactions: M:F.95, M:V.99, M:W.120, M:W.120, M:V.124, M:I.126, M:L.207 Hydrogen bonds: M:W.36, M:W.36, M:G.39, M:S.111, M:N.213 Salt bridges: M:H.102, M:R.105, M:R.105 pi-Cation interactions: M:R.105 Metal complexes: M:H.102, M:H.203

29 x 3PE: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE(Non-covalent)

3PE.7: 10 residues within 4Å: Chain C: P.14, I.15, S.17, T.18 Chain M: F.118, G.198, L.202, A.205, Q.209 Chain P: P.122 Ligand excluded by PLIP 3PE.8: 9 residues within 4Å: Chain C: F.118, L.202, A.205, A.206, Q.209 Chain F: P.122 Chain M: P.14, I.15, T.18 Ligand excluded by PLIP 3PE.9: 15 residues within 4Å: Chain C: F.324, R.325, P.326, I.327, Y.328, I.374, L.375, V.378, G.379, I.382 Chain F: L.16, H.20, L.24, Y.35 Ligands: 3PE.15 Ligand excluded by PLIP 3PE.10: 10 residues within 4Å: Chain C: Y.100, F.104, W.279, L.282, P.283, G.343, W.344, C.347, Q.348, F.365 Ligand excluded by PLIP 3PE.11: 12 residues within 4Å: Chain C: W.35, Y.108, Y.109, S.323, F.332, W.333 Chain F: Y.31, Y.78 Chain G: N.41, S.44, L.48 Ligands: CDL.12 Ligand excluded by PLIP 3PE.15: 11 residues within 4Å: Chain C: P.326, I.327, I.331 Chain F: L.16, Q.19, H.20, S.23, K.26, R.27 Chain G: I.43 Ligands: 3PE.9 Ligand excluded by PLIP 3PE.16: 6 residues within 4Å: Chain D: Y.286 Chain E: F.110 Chain G: K.21, V.22, M.23, T.24 Ligand excluded by PLIP 3PE.20: 5 residues within 4Å: Chain C: F.118 Chain F: Q.118, R.119, I.121 Chain M: R.7 Ligand excluded by PLIP 3PE.24: 6 residues within 4Å: Chain E: L.131, V.134, L.135 Chain J: L.32 Chain M: T.166, W.170 Ligand excluded by PLIP 3PE.25: 13 residues within 4Å: Chain M: W.35, Y.108, Y.109, S.323, Q.329, W.333, L.336 Chain P: Y.31, Y.78 Chain Q: N.41, L.48, L.49 Ligands: CDL.31 Ligand excluded by PLIP 3PE.26: 11 residues within 4Å: Chain M: P.326, I.327, G.330, I.331, L.334 Chain P: Q.19, H.20, S.23, K.26, R.27 Chain Q: I.43 Ligand excluded by PLIP 3PE.27: 5 residues within 4Å: Chain M: Y.252 Chain N: K.80, G.81, I.82, I.274 Ligand excluded by PLIP 3PE.37: 9 residues within 4Å: Chain U: F.172, T.180, M.181, H.182, L.192, L.200, V.284, F.287 Ligands: 3PE.43 Ligand excluded by PLIP 3PE.38: 11 residues within 4Å: Chain U: H.236, F.240, W.290, L.299, D.300, T.303, Y.306 Chain W: M.95, F.98, W.102 Ligands: 3PE.51 Ligand excluded by PLIP 3PE.40: 9 residues within 4Å: Chain U: Y.336, L.341, V.344, F.348, Q.413, W.417 Chain X: M.1, T.3 Ligands: 3PE.47 Ligand excluded by PLIP 3PE.41: 7 residues within 4Å: Chain 3: V.71, F.72 Chain U: L.411, C.469, V.472, T.475 Chain X: I.16 Ligand excluded by PLIP 3PE.42: 7 residues within 4Å: Chain U: F.218 Chain W: G.32, Y.35, M.36, S.47 Chain Z: L.93 Ligands: 3PE.49 Ligand excluded by PLIP 3PE.43: 8 residues within 4Å: Chain U: F.172, M.181, F.196 Chain W: Y.84, L.88, V.94 Ligands: 3PE.37, 3PE.52 Ligand excluded by PLIP 3PE.45: 4 residues within 4Å: Chain U: W.452, L.455 Chain V: L.19 Ligands: 3PE.55 Ligand excluded by PLIP 3PE.46: 4 residues within 4Å: Chain 1: V.17 Chain U: A.327 Chain V: V.53, I.78 Ligand excluded by PLIP 3PE.47: 9 residues within 4Å: Chain Q: K.28, P.31 Chain U: Y.336 Chain V: L.51, S.55, L.58, R.62, S.63 Ligands: 3PE.40 Ligand excluded by PLIP 3PE.48: 15 residues within 4Å: Chain U: F.97, P.98, R.99, L.100, I.103, L.155, V.158, L.162 Chain W: H.10, V.12, A.25, W.60, W.61, H.74, F.89 Ligand excluded by PLIP 3PE.49: 13 residues within 4Å: Chain U: H.154, F.218 Chain W: Y.184, A.187, T.190, I.191, F.201, G.205, F.206, F.209 Chain Z: L.93, F.94 Ligands: 3PE.42 Ligand excluded by PLIP 3PE.50: 14 residues within 4Å: Chain W: M.57, W.61, L.65, T.69, H.74, F.86, F.89, I.213, F.217, R.224, H.229, H.234, V.236, G.237 Ligand excluded by PLIP 3PE.51: 9 residues within 4Å: Chain U: D.230 Chain W: F.98, W.102, F.105, H.106, A.110, T.112, F.254 Ligands: 3PE.38 Ligand excluded by PLIP 3PE.52: 4 residues within 4Å: Chain W: R.83, I.87, V.250 Ligands: 3PE.43 Ligand excluded by PLIP 3PE.53: 6 residues within 4Å: Chain 3: V.79, V.86 Chain U: L.37 Chain X: I.29, F.30, G.31 Ligand excluded by PLIP 3PE.55: 14 residues within 4Å: Chain 1: A.30, W.34, H.37, E.41 Chain U: T.356, F.432, L.435 Chain V: L.19, G.20, F.21, H.36, H.37, F.40 Ligands: 3PE.45 Ligand excluded by PLIP 3PE.58: 6 residues within 4Å: Chain 2: Y.50, R.54, Y.57 Ligands: PC1.36, CDL.39, PC1.56 Ligand excluded by PLIP

2 x HEC: HEME C(Covalent)

HEC.13: 19 residues within 4Å: Chain D: V.101, C.102, C.105, H.106, N.170, A.173, Y.174, P.175, P.176, I.181, R.185, Y.191, L.195, L.196, F.218, A.224, M.225, M.228, V.251 19 PLIP interactions: 19 interactions with chain D, Hydrophobic interactions: D:V.101, D:N.170, D:A.173, D:P.175, D:P.176, D:I.181, D:L.195, D:L.196, D:L.196, D:F.218, D:A.224, D:M.225, D:V.251 Hydrogen bonds: D:Y.191, D:A.224 Salt bridges: D:R.185 pi-Stacking: D:H.106, D:H.106 Metal complexes: D:H.106 HEC.28: 18 residues within 4Å: Chain N: V.101, C.102, C.105, H.106, N.170, A.173, Y.174, P.175, P.176, I.181, R.185, Y.191, L.195, L.196, F.218, A.224, M.225, M.228 16 PLIP interactions: 16 interactions with chain N, Hydrophobic interactions: N:V.101, N:N.170, N:P.175, N:P.176, N:I.181, N:L.195, N:L.196, N:L.196, N:F.218, N:A.224 Hydrogen bonds: N:Y.191, N:Y.191 Salt bridges: N:R.185 pi-Stacking: N:H.106, N:H.106 Metal complexes: N:H.106

2 x HEA: HEME-A(Non-covalent)

HEA.32: 26 residues within 4Å: Chain U: W.129, W.239, V.246, Y.247, H.292, H.293, T.311, A.315, G.319, I.322, F.350, G.354, I.358, L.360, A.361, D.366, H.370, V.375, H.378, F.379, V.382, L.383, R.440 Chain V: I.46, I.89, L.90 27 PLIP interactions: 24 interactions with chain U, 3 interactions with chain V, Hydrophobic interactions: U:W.129, U:W.239, U:V.246, U:V.246, U:A.315, U:I.322, U:F.350, U:I.358, U:A.361, U:F.379, U:F.379, U:V.382, U:L.383, V:I.46, V:I.89, V:L.90 Hydrogen bonds: U:Y.247, U:Y.247, U:D.366, U:R.440 Salt bridges: U:H.370, U:R.440 pi-Stacking: U:H.293 pi-Cation interactions: U:H.243, U:H.243, U:H.293 Metal complexes: U:H.378 HEA.33: 30 residues within 4Å: Chain U: G.24, A.25, G.28, V.29, T.32, S.35, I.38, R.39, Y.57, I.61, H.64, A.65, M.68, I.69, G.128, W.129, Y.373, F.379, H.380, L.383, S.384, L.391, F.392, V.423, F.427, R.440, R.441, S.460, I.467, F.470 25 PLIP interactions: 25 interactions with chain U, Hydrophobic interactions: U:I.61, U:A.65, U:M.68, U:F.379, U:F.379, U:L.383, U:L.391, U:F.392, U:F.392, U:F.427, U:I.467, U:F.470, U:F.470 Hydrogen bonds: U:W.129, U:S.384, U:R.441 Salt bridges: U:R.440, U:R.441 pi-Stacking: U:H.64, U:F.379, U:H.380, U:H.380, U:F.427 Metal complexes: U:H.64, U:H.380

1 x CU: COPPER (II) ION(Non-covalent)

CU.34: 3 residues within 4Å: Chain U: H.243, H.292, H.293 3 PLIP interactions: 3 interactions with chain U Metal complexes: U:H.243, U:H.292, U:H.293

1 x MG: MAGNESIUM ION(Non-covalent)

MG.35: 4 residues within 4Å: Chain U: H.370, D.371 Chain V: D.196, E.221 3 PLIP interactions: 1 interactions with chain V, 2 interactions with chain U Metal complexes: V:E.221, U:H.370, U:D.371

1 x CUA: DINUCLEAR COPPER ION(Covalent)

CUA.44: 6 residues within 4Å: Chain V: H.184, C.219, E.221, C.223, H.227, M.230 7 PLIP interactions: 7 interactions with chain V Metal complexes: V:H.184, V:C.219, V:C.219, V:E.221, V:C.223, V:C.223, V:H.227

1 x LYS: LYSINE(Non-covalent)

LYS.57: 1 residues within 4Å: Chain 2: K.65 1 PLIP interactions: 1 interactions with chain 2, Hydrogen bonds: 2:K.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maldonado, M. et al., Atomic structures of respiratory complex III 2 , complex IV, and supercomplex III 2 -IV from vascular plants. Elife (2021)

Release Date

2021-01-20

Peptides

Mitochondrial-processing peptidase subunit beta, mitochondrial isoform X1: AK
Alpha-MPP: BL
COB: CM
cytochrome c1-2, heme protein, mitochondrial: DN
Cytochrome b-c1 complex subunit Rieske, mitochondrial: EO
Cytochrome b-c1 complex subunit 7: FP
cytochrome b-c1 complex subunit 8: GQ
Cytochrome b-c1 complex subunit 6: HR
cytochrome b-c1 complex subunit 9: IS
QCR10: JT
COX1: U
Cytochrome c oxidase subunit 2: V
COX3: W
COX4: X
cytochrome c oxidase subunit 5b-2, mitochondrial: Y
cytochrome c oxidase subunit 6a, mitochondrial: Z
cytochrome c oxidase subunit 6b-1: 0
Cytochrome c oxidase subunit 5C: 1
COX7a: 2
COX7c: 3

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

K
M

B
B

L
N

C
C

M
O

D
D

N
P

E
E

O
Q

F
F

P
R

G
G

Q
S

H
H

R
T

I
J

S
V

J
K

T
W

U
a

V
b

W
c

X
d

Y
e

Z
f

0
g

1
h

2
i

3
j

Membrane

We predict this structure to be a membrane protein.
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Mitochondrial-processing peptidase subunit beta, mitochondrial isoform X1

Alpha-MPP

COB

cytochrome c1-2, 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

cytochrome b-c1 complex subunit 9

QCR10

COX1

Cytochrome c oxidase subunit 2

COX3

COX4

cytochrome c oxidase subunit 5b-2, mitochondrial

cytochrome c oxidase subunit 6a, mitochondrial

cytochrome c oxidase subunit 6b-1

Cytochrome c oxidase subunit 5C

COX7a

COX7c

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