MolNFT v1 · #167140 · protein
Structure of the bovine BBSOME:ARL6:GTP complex
6VBV · Bardet-biedl syndrome 18 protein: “Structure of the bovine BBSOME:ARL6:GTP complex”. Electron microscopy, 2 ligands (GTP, CA), 20 pockets (best druggability 0.87). MolNFT v1 #167140 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6VBV
- Type
- protein
- Length
- 4,000 residues
- Chains
- 9
- 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, Q0IIM2
- Ligands
- GTP, CA
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 9 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 0 | Bardet-biedl syndrome 18 protein | protein | 52 | 37% helix, 2% strand | G3N2W1 |
| 1 | BBS1 domain-containing protein | protein | 486 | 8% helix, 47% strand | E1BN34 |
| 2 | Bardet-biedl syndrome 2 protein homolog | protein | 659 | 25% helix, 34% strand | Q32L13 |
| 4 | Bardet-biedl syndrome 4 protein homolog | protein | 391 | 72% helix, 0% strand | Q1JQ97 |
| 5 | Bardet-biedl syndrome 5 protein homolog | protein | 300 | 14% helix, 30% strand | A6QLF9 |
| 7 | Bardet-biedl syndrome 7 protein homolog | protein | 706 | 22% helix, 31% strand | F1MB52 |
| 8 | Tetratricopeptide repeat domain 8 | protein | 475 | 65% helix, 1% strand | F1N4X0 |
| 9 | Bardet-biedl syndrome 9 | protein | 764 | 25% helix, 32% strand | E1BHJ5 |
| 3 | ADP-ribosylation factor-like protein 6 | protein | 167 | 29% helix, 19% strand | Q0IIM2 |
Ligands and binding sites
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 877 | 0.87 | 0.90 | 114 | empty |
| 2 | 774 | 0.85 | 0.88 | 72 | empty |
| 3 | 1105 | 0.84 | 0.85 | 109 | empty |
| 4 | 1172 | 0.83 | 0.84 | 100 | empty |
| 5 | 1009 | 0.79 | 0.80 | 68 | empty |
Interfaces
21 interfaces between chains.
- 5–9 · 3045 Ų buried · 38 hydrogen bonds · protein-protein
- 2–7 · 2876 Ų buried · 34 hydrogen bonds · protein-protein
- 8–9 · 2728 Ų buried · 25 hydrogen bonds · protein-protein
- 1–9 · 2477 Ų buried · 15 hydrogen bonds · protein-protein
- 1–8 · 2167 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6VBV · Structure of the bovine BBSome:ARL6:GTP complex · the same entry in another collection · chain 3 against 3, TM-score 1.00
- Q0IIM2 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor-like protein 6 (Q0IIM2) · a predicted model of the same protein · chain 3 against A, TM-score 0.97
- 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 0.89
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
- Every structure of UniProt Q0IIM2
- Elsewhere: RCSB PDB 6VBV · PDBe 6VBV · UniProt G3N2W1 · UniProt E1BN34 · UniProt Q32L13 · UniProt Q1JQ97 · UniProt A6QLF9 · UniProt F1MB52 · UniProt F1N4X0 · UniProt E1BHJ5 · UniProt Q0IIM2
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