Research workbench

Rhodobacter sphaeroides BC1 with stigmatellin and antimycin

Analyse Rhodobacter sphaeroides BC1 with stigmatellin and antimycin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5KLI
Type: protein
Length: 3,452 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome B; Cytochrome C1; Ubiquinol-cytochrome C reductase iron-sulfur subunit
EC: 1.10.2.2
UniProt: Q02761, Q02760, Q02762
Ligands: HEM, SMA, ANJ, LOP, HEC, FES, SR
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 3 distinct chains · 50% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, K, O	Cytochrome B	protein	428	67% helix, 2% strand	Q02761
B, F, L, P	Cytochrome C1	protein	256	39% helix, 7% strand	Q02760
C, G, M, Q	Ubiquinol-cytochrome C reductase iron-sulfur subunit (EC 1.10.2.2)	protein	179	24% helix, 28% strand	Q02762

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains A, E, K, O
SMA · Stigmatellin A · ligand · 4 copies · chains A, G, C, E, K, Q, M, O
ANJ · (2R,3S,6S,7R,8R)-3-{[3-(formylamino)-2-hydroxybenzoyl]amino}-8-hexyl-2,6-dimethyl-4,9-dioxo-1,5-dioxonan-7-yl (2S)-2-methylbutanoate · ligand · 4 copies · chains A, E, K, O
LOP · (1R)-2-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(dodecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate · ligand · 4 copies · chains A, E, K, O
HEC · Heme C · ligand · 4 copies · chains B, F, L, P
FES · Fe2/s2 (inorganic) cluster · ligand · 4 copies · chains C, G, M, Q
SR · Strontium ion · metal · 6 copies · chains B, F, E, K, L, P

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	878	0.88	0.91	94	HEM
2	1010	0.88	0.89	105	HEM
3	1173	0.88	0.89	121	HEM
4	1192	0.88	0.89	121	HEM
5	450	0.80	0.88	44	HEM, ANJ

Interfaces

26 interfaces between chains.

A–B · 2044 Å² buried · 18 hydrogen bonds · protein-protein
O–P · 2039 Å² buried · 20 hydrogen bonds · protein-protein
K–L · 2031 Å² buried · 18 hydrogen bonds · protein-protein
E–F · 2025 Å² buried · 20 hydrogen bonds · protein-protein
K–O · 1566 Å² buried · 21 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 cofactor, 8 disulfide (heme c attachment, disulfide).

Compared structures

5KLI · Rhodobacter sphaeroides bc1 with stigmatellin and antimycin · the same entry in another collection · chain Q against Q, 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 Q02761
Every structure of UniProt Q02760
Every structure of UniProt Q02762
Elsewhere: RCSB PDB 5KLI · PDBe 5KLI · UniProt Q02761 · UniProt Q02760 · UniProt Q02762

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