MolNFT v1 · #124638 · protein

Rhodobacter sphaeroides BC1 with famoxadone

5KKZ · Cytochrome B: “Rhodobacter sphaeroides BC1 with famoxadone”. X-ray diffraction, 7 ligands (HEM, FMX, ASC), 20 pockets (best druggability 0.88). MolNFT v1 #124638 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5KKZ
Type: protein
Length: 3,456 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, FMX, ASC, 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	429	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	26% helix, 27% strand	Q02762

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains A, E, K, O
FMX · Famoxadone · ligand · 4 copies · chains A, E, K, O
ASC · Ascorbic acid · ligand · 4 copies · chains A, G, C, E, K, Q, M, 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 A, B, F, E, K, L, P
BOG · octyl beta-D-glucopyranoside · additive · 4 copies · chains A, B, E, F, K, L, O, 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	660	0.88	0.92	68	HEM, BOG
2	691	0.88	0.91	72	HEM, SR, BOG
3	685	0.87	0.91	74	HEM, BOG
4	661	0.87	0.91	68	HEM, BOG
5	1088	0.82	0.83	107	ASC, HEC

Interfaces

27 interfaces between chains.

A–B · 1967 Å² buried · 17 hydrogen bonds · protein-protein
E–F · 1962 Å² buried · 17 hydrogen bonds · protein-protein
K–L · 1957 Å² buried · 17 hydrogen bonds · protein-protein
O–P · 1951 Å² buried · 18 hydrogen bonds · protein-protein
K–O · 1555 Å² buried · 22 hydrogen bonds · protein-protein

Modifications

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

Compared structures

5KKZ · Rhodobacter sphaeroides bc1 with famoxadone · 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 5KKZ · PDBe 5KKZ · UniProt Q02761 · UniProt Q02760 · UniProt Q02762

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