MolNFT v1 · #167139 · protein

Structure of the bovine bbsome complex

6VBU · Bardet-biedl syndrome 18 protein: “Structure of the bovine bbsome complex”. Electron microscopy, 1 ligand (CA), 20 pockets (best druggability 0.87). MolNFT v1 #167139 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6VBU
Type: protein
Length: 3,820 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bardet-biedl syndrome 18 protein; BBS1 domain-containing protein; Bardet-biedl syndrome 2…
UniProt: G3N2W1, E1BN34, Q32L13, Q1JQ97, A6QLF9, F1MB52, F1N4X0, E1BHJ5
Ligands: CA
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 8 distinct chains · 31% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
0	Bardet-biedl syndrome 18 protein	protein	52	35% helix, 4% strand	G3N2W1
1	BBS1 domain-containing protein	protein	486	8% helix, 45% strand	E1BN34
2	Bardet-biedl syndrome 2 protein homolog	protein	659	25% helix, 34% strand	Q32L13
4	Bardet-biedl syndrome 4 protein homolog	protein	386	73% helix, 0% strand	Q1JQ97
5	Bardet-biedl syndrome 5 protein homolog	protein	300	15% helix, 35% strand	A6QLF9
7	Bardet-biedl syndrome 7 protein homolog	protein	698	22% helix, 34% strand	F1MB52
8	Bardet-biedl syndrome 8 protein	protein	475	64% helix, 1% strand	F1N4X0
9	Bardet-biedl syndrome 9	protein	764	25% helix, 34% strand	E1BHJ5

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains 2

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	734	0.87	0.90	85	empty
2	915	0.86	0.88	87	empty
3	1071	0.85	0.86	102	empty
4	1152	0.83	0.84	98	empty
5	1004	0.78	0.80	74	empty

Interfaces

19 interfaces between chains.

2–7 · 2950 Å² buried · 38 hydrogen bonds · protein-protein
5–9 · 2913 Å² buried · 39 hydrogen bonds · protein-protein
8–9 · 2676 Å² buried · 23 hydrogen bonds · protein-protein
1–9 · 2376 Å² buried · 15 hydrogen bonds · protein-protein
1–8 · 2123 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

6VBU · Structure of the bovine BBSome complex · the same entry in another collection · chain 9 against 9, 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 4 against A, TM-score 0.91

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 E1BN34
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
Elsewhere: RCSB PDB 6VBU · PDBe 6VBU · UniProt G3N2W1 · UniProt E1BN34 · UniProt Q32L13 · UniProt Q1JQ97 · UniProt A6QLF9 · UniProt F1MB52 · UniProt F1N4X0 · UniProt E1BHJ5

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