Research workbench

Cryo-EM structure of apo-bbsome

Analyse Cryo-EM structure of apo-bbsome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6VNW
Type: protein
Length: 3,831 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bardet-biedl syndrome 18 protein; Bardet-biedl syndrome 2 protein homolog; Bardet-biedl…
UniProt: G3N2W1, Q32L13, Q1JQ97, A6QLF9, F1MB52, F1N4X0, E1BHJ5, E1BN34
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 8 distinct chains · 32% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Bardet-biedl syndrome 18 protein	protein	52	37% helix, 2% strand	G3N2W1
B	Bardet-biedl syndrome 2 protein homolog	protein	659	25% helix, 33% strand	Q32L13
E	Bardet-biedl syndrome 4 protein homolog	protein	388	72% helix, 0% strand	Q1JQ97
G	Bardet-biedl syndrome 5 protein homolog	protein	300	14% helix, 30% strand	A6QLF9
C	Bardet-biedl syndrome 7 protein homolog	protein	665	23% helix, 30% strand	F1MB52
F	Tetratricopeptide repeat domain 8	protein	475	66% helix, 1% strand	F1N4X0
I	Bardet-biedl syndrome 9	protein	764	25% helix, 32% strand	E1BHJ5
D	BBS1 domain-containing protein	protein	528	11% helix, 26% strand	E1BN34

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	796	0.86	0.89	95	empty
2	1115	0.86	0.87	126	empty
3	830	0.86	0.88	85	empty
4	1174	0.82	0.83	100	empty
5	621	0.81	0.86	67	empty

Interfaces

19 interfaces between chains.

G–I · 2999 Å² buried · 35 hydrogen bonds · protein-protein
F–I · 2750 Å² buried · 25 hydrogen bonds · protein-protein
I–D · 2389 Å² buried · 15 hydrogen bonds · protein-protein
F–D · 2190 Å² buried · 19 hydrogen bonds · protein-protein
H–F · 1774 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

6VNW · Cryo-EM structure of apo-BBSome · the same entry in another collection · chain D against D, TM-score 1.00
Q1JQ97 · AlphaFold monomer V2.0 prediction for bardet-biedl syndrome 4 protein homolog (Q1JQ97) · a predicted model of the same protein · chain E against A, TM-score 0.90

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 G3N2W1
Every structure of UniProt Q32L13
Every structure of UniProt Q1JQ97
Every structure of UniProt A6QLF9
Every structure of UniProt F1MB52
Every structure of UniProt F1N4X0
Every structure of UniProt E1BHJ5
Every structure of UniProt E1BN34
Elsewhere: RCSB PDB 6VNW · PDBe 6VNW · UniProt G3N2W1 · UniProt Q32L13 · UniProt Q1JQ97 · UniProt A6QLF9 · UniProt F1MB52 · UniProt F1N4X0 · UniProt E1BHJ5 · UniProt E1BN34

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