Research workbench

Complex III2 from candida albicans, inz-5 bound

Analyse Complex III2 from candida albicans, inz-5 bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7RJE
Type: protein
Length: 3,818 residues
Chains: 18
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome B; Ubiquinol--cytochrome-C reductase subunit; Cytochrome B-C1 complex subunit…
EC: 7.1.1.8
UniProt: P0C8L0, A0A1D8PP59, P83782, A0A1D8PHA3, Q5ABS1, A0A1D8PHA2, A0A1D8PJT8, A0A1D8PLP3, A0A1D8PJX3
Ligands: HEM, ZL5, HEC, FES
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 9 distinct chains · 53% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
K, T	Cytochrome B	protein	384	75% helix, 2% strand	P0C8L0
A, E	Ubiquinol--cytochrome-C reductase subunit	protein	417	47% helix, 19% strand	A0A1D8PP59
B, L	Cytochrome B-C1 complex subunit 2, mitochondrial	protein	364	39% helix, 19% strand	P83782
D, N	Ubiquinol--cytochrome-C reductase catalytic subunit	protein	243	42% helix, 8% strand	A0A1D8PHA3
G, P	Cytochrome B-C1 complex subunit 7	protein	122	70% helix, 1% strand	Q5ABS1
F, O	Ubiquinol--cytochrome-C reductase subunit 8	protein	88	63% helix, 8% strand	A0A1D8PHA2
H, Q	Ubiquinol--cytochrome-C reductase subunit 6	protein	72	75% helix, 0% strand	A0A1D8PJT8
I, R	Ubiquinol--cytochrome-C reductase subunit 9	protein	38	89% helix, 0% strand	A0A1D8PLP3
C, M	Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 7.1.1.8)	protein	181	29% helix, 14% strand	A0A1D8PJX3

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains K, T
ZL5 · 3-[2-fluoro-5-(trifluoromethyl)phenyl]-7-methyl-1-[(2-methyl-2H-tetrazol-5-yl)methyl]-1H-indazole · ligand · 2 copies · chains K, T
HEC · Heme C · ligand · 2 copies · chains D, N
FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains C, M

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	323	0.86	0.95	44	HEM
2	339	0.84	0.93	42	HEM
3	925	0.80	0.82	135	FES
4	925	0.79	0.81	128	FES
5	376	0.79	0.88	48	HEM

Interfaces

53 interfaces between chains.

K–G · 1907 Å² buried · 11 hydrogen bonds · protein-protein
T–P · 1894 Å² buried · 10 hydrogen bonds · protein-protein
E–L · 1769 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1768 Å² buried · 11 hydrogen bonds · protein-protein
T–N · 1668 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 cofactor, 1 covalent (heme c attachment, heme attachment, covalent ligand).

Compared structures

7RJE · Complex III2 from Candida albicans, Inz-5 bound · the same entry in another collection · chain M against M, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P0C8L0
Every structure of UniProt A0A1D8PP59
Every structure of UniProt P83782
Every structure of UniProt A0A1D8PHA3
Every structure of UniProt Q5ABS1
Every structure of UniProt A0A1D8PHA2
Every structure of UniProt A0A1D8PJT8
Every structure of UniProt A0A1D8PLP3
Every structure of UniProt A0A1D8PJX3
Elsewhere: RCSB PDB 7RJE · PDBe 7RJE · UniProt P0C8L0 · UniProt A0A1D8PP59 · UniProt P83782 · UniProt A0A1D8PHA3 · UniProt Q5ABS1 · UniProt A0A1D8PHA2 · UniProt A0A1D8PJT8 · UniProt A0A1D8PLP3 · UniProt A0A1D8PJX3

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.