SMTL ID : 9cg3.1

Human kidney respiratory complex III

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Covalent)

FES.1: 8 residues within 4Å: Chain B: C.217, H.219, C.222, C.236, C.238, H.239, S.241, P.253 5 PLIP interactions: 5 interactions with chain B, Metal complexes: B:C.217, B:H.219, B:H.219, B:C.236, B:H.239 FES.5: 9 residues within 4Å: Chain K: C.217, H.219, L.220, C.222, C.236, C.238, H.239, S.241, P.253 3 PLIP interactions: 3 interactions with chain K, Metal complexes: K:C.217, K:H.219, K:C.236

2 x HEC: HEME C(Non-covalent)(Covalent)

HEC.2: 23 residues within 4Å: Chain G: V.120, C.121, S.123, C.124, H.125, N.189, A.192, P.194, P.195, L.197, I.200, R.204, Y.210, L.214, L.215, F.237, I.242, A.243, M.244, P.247, I.248, V.270, L.274 18 PLIP interactions: 18 interactions with chain G, Hydrophobic interactions: G:N.189, G:A.192, G:P.195, G:L.197, G:I.200, G:L.214, G:L.215, G:I.242, G:I.242, G:A.243, G:I.248, G:V.270, G:V.270, G:L.274 Hydrogen bonds: G:Y.210, G:A.243 Salt bridges: G:R.204 Metal complexes: G:H.125 HEC.6: 23 residues within 4Å: Chain P: V.120, C.121, C.124, H.125, N.189, A.192, L.193, P.194, P.195, L.197, I.200, R.204, Y.210, V.211, L.214, L.215, F.237, I.242, A.243, M.244, P.247, I.248, V.270 18 PLIP interactions: 18 interactions with chain P, Hydrophobic interactions: P:V.120, P:A.192, P:P.195, P:L.197, P:I.200, P:V.211, P:L.214, P:L.215, P:L.215, P:I.242, P:A.243, P:P.247, P:I.248, P:V.270 Hydrogen bonds: P:Y.210, P:A.243 Salt bridges: P:R.204 Metal complexes: P:H.125

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

HEM.3: 22 residues within 4Å: Chain H: L.41, Q.44, I.45, G.48, L.49, L.51, A.52, Y.55, I.66, R.80, H.83, A.87, T.126, G.130, Y.131, L.133, P.134, F.179, H.182, F.183, P.186, Y.273 16 PLIP interactions: 16 interactions with chain H, Hydrophobic interactions: H:L.41, H:Q.44, H:L.49, H:L.51, H:Y.55, H:Y.55, H:I.66, H:T.126, H:L.133, H:F.179, H:F.183, H:F.183 Salt bridges: H:R.80, H:R.80 Metal complexes: H:H.83, H:H.182 HEM.4: 25 residues within 4Å: Chain H: W.31, G.34, S.35, L.37, G.38, F.90, L.94, H.97, I.98, R.100, S.106, Y.109, T.112, W.113, G.116, L.119, L.120, I.189, A.193, H.196, L.197, L.200, S.205, N.206, L.301 23 PLIP interactions: 23 interactions with chain H, Hydrophobic interactions: H:L.37, H:L.37, H:F.90, H:T.112, H:W.113, H:W.113, H:L.119, H:L.120, H:I.189, H:A.193, H:L.197, H:L.200, H:L.200, H:L.301 Hydrogen bonds: H:W.31, H:G.34, H:S.35, H:S.106, H:N.206 Salt bridges: H:H.97, H:R.100, H:R.100 Metal complexes: H:H.97 HEM.7: 21 residues within 4Å: Chain Q: Q.44, I.45, G.48, L.49, L.51, A.52, Y.55, I.66, R.80, H.83, A.87, T.126, G.130, Y.131, L.133, P.134, F.179, H.182, F.183, P.186, Y.273 13 PLIP interactions: 13 interactions with chain Q, Hydrophobic interactions: Q:Q.44, Q:L.51, Q:Y.55, Q:I.66, Q:L.133, Q:L.133, Q:F.179, Q:F.183, Q:F.183 Salt bridges: Q:R.80, Q:R.80 Metal complexes: Q:H.83, Q:H.182 HEM.8: 23 residues within 4Å: Chain Q: W.31, G.34, S.35, L.37, F.90, L.94, H.97, I.98, R.100, S.106, Y.109, T.112, W.113, G.116, L.119, L.120, I.189, A.193, H.196, L.197, L.200, S.205, N.206 23 PLIP interactions: 23 interactions with chain Q, Hydrophobic interactions: Q:L.37, Q:L.37, Q:F.90, Q:T.112, Q:W.113, Q:W.113, Q:L.119, Q:L.119, Q:L.120, Q:I.189, Q:A.193, Q:L.197, Q:L.200, Q:L.200 Hydrogen bonds: Q:G.34, Q:S.35, Q:S.106, Q:N.206 Salt bridges: Q:H.97, Q:R.100, Q:R.100 pi-Cation interactions: Q:R.100 Metal complexes: Q:H.97

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Z. et al., Human kidney respiratory complex III. To Be Published

Release Date

2025-08-06

Peptides

Cytochrome b-c1 complex subunit 8: AT
Cytochrome b-c1 complex subunit Rieske, mitochondrial: BK
Cytochrome b-c1 complex subunit 9: CL
Cytochrome b-c1 complex subunit 6, mitochondrial: DM
Cytochrome b-c1 complex subunit 7: EN
Cytochrome b-c1 complex subunit 10: FO
Cytochrome c1, heme protein, mitochondrial: GP
Cytochrome b: HQ
Cytochrome b-c1 complex subunit 2, mitochondrial: IR
Cytochrome b-c1 complex subunit 1, mitochondrial: JS

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

T
N

B
C

K
P

C
D

L
Q

D
E

M
R

E
F

N
S

F
G

O
T

G
H

P
U

H
J

Q
V

I
K

R
W

J
L

S
Y

Membrane

We predict this structure to be a membrane protein.
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Cytochrome b-c1 complex subunit 8

Cytochrome b-c1 complex subunit Rieske, mitochondrial

Cytochrome b-c1 complex subunit 9

Cytochrome b-c1 complex subunit 6, mitochondrial

Cytochrome b-c1 complex subunit 7

Cytochrome b-c1 complex subunit 10

Cytochrome c1, heme protein, mitochondrial

Cytochrome b

Cytochrome b-c1 complex subunit 2, mitochondrial

Cytochrome b-c1 complex subunit 1, mitochondrial