Research workbench

Complex III2 from candida albicans, inhibitor free

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

PDB: 7RJA
Type: protein
Length: 3,812 residues
Chains: 18
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquinol--cytochrome-C reductase subunit; Cytochrome B; Ubiquinol--cytochrome-C…
EC: 7.1.1.8
UniProt: A0A1D8PP59, P0C8L0, A0A1D8PHA3, Q5ABS1, A0A1D8PHA2, A0A1D8PJT8, A0A1D8PLP3, A0A1D8PJX3, P83782
Ligands: HEM, U10, HEC, FES
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 9 distinct chains · 52% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, J	Ubiquinol--cytochrome-C reductase subunit	protein	416	47% helix, 16% strand	A0A1D8PP59
K, T	Cytochrome B	protein	383	72% helix, 2% strand	P0C8L0
D, N	Ubiquinol--cytochrome-C reductase catalytic subunit	protein	244	41% helix, 8% strand	A0A1D8PHA3
G, Q	Cytochrome B-C1 complex subunit 7	protein	122	68% helix, 1% strand	Q5ABS1
F, P	Ubiquinol--cytochrome-C reductase subunit 8	protein	85	55% helix, 8% strand	A0A1D8PHA2
H, R	Ubiquinol--cytochrome-C reductase subunit 6	protein	72	75% helix, 0% strand	A0A1D8PJT8
I, S	Ubiquinol--cytochrome-C reductase subunit 9	protein	39	82% 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
B, L	Cytochrome B-C1 complex subunit 2, mitochondrial	protein	364	41% helix, 19% strand	P83782

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains K, T
U10 · Ubiquinone-10 · ligand · 4 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	554	0.83	0.88	65	HEM
2	607	0.82	0.87	66	HEM
3	435	0.80	0.87	52	HEM, U10
4	1095	0.77	0.79	112	HEC
5	1089	0.77	0.79	98	empty

Interfaces

47 interfaces between chains.

T–Q · 1856 Å² buried · 11 hydrogen bonds · protein-protein
K–G · 1837 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 1791 Å² buried · 13 hydrogen bonds · protein-protein
J–L · 1790 Å² buried · 15 hydrogen bonds · protein-protein
T–N · 1766 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 cofactor, 2 covalent, 2 disulfide (heme c attachment, heme attachment, covalent ligand, disulfide).

Compared structures

P0C8L0 · AlphaFold monomer V2.0 prediction for cytochrome B (P0C8L0) · a predicted model of the same protein · chain T against A, TM-score 0.99
P83782 · AlphaFold monomer V2.0 prediction for cytochrome B-C1 complex subunit 2, mitochondrial… · a predicted model of the same protein · chain B against A, TM-score 0.98

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 A0A1D8PP59
Every structure of UniProt P0C8L0
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
Every structure of UniProt P83782
Elsewhere: RCSB PDB 7RJA · PDBe 7RJA · UniProt A0A1D8PP59 · UniProt P0C8L0 · UniProt A0A1D8PHA3 · UniProt Q5ABS1 · UniProt A0A1D8PHA2 · UniProt A0A1D8PJT8 · UniProt A0A1D8PLP3 · UniProt A0A1D8PJX3 · UniProt P83782

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