Research workbench
Crystal structure of BBS1N in complex with ARL6DN, soaked with mercury
Analyse Crystal structure of BBS1N in complex with ARL6DN, soaked with mercury in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4V0N
- Type
- protein
- Length
- 1,927 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arf-like small GTPase; Bardet-biedl syndrome 1 protein
- UniProt
- A8JF99, A8JEA1
- Ligands
- GTP, HG, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 4% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Arf-like small GTPase | protein | 166 | 31% helix, 26% strand | A8JF99 |
| B | Bardet-biedl syndrome 1 protein | protein | 330 | 1% helix, 56% strand | A8JEA1 |
| D | Bardet-biedl syndrome 1 protein | protein | 304 | 1% helix, 59% strand | A8JEA1 |
| F | Bardet-biedl syndrome 1 protein | protein | 304 | 1% helix, 59% strand | A8JEA1 |
| H | Bardet-biedl syndrome 1 protein | protein | 325 | 1% helix, 56% strand | A8JEA1 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains A, C, E, G
- HG · Mercury (II) ion · metal · 57 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 4 copies · chains A, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 974 | 0.81 | 0.83 | 87 | HG |
| 2 | 810 | 0.80 | 0.84 | 80 | HG |
| 3 | 1048 | 0.78 | 0.80 | 77 | HG |
| 4 | 1134 | 0.77 | 0.79 | 80 | HG |
| 5 | 746 | 0.72 | 0.78 | 69 | HG |
Interfaces
14 interfaces between chains.
- E–F · 675 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 662 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 644 Ų buried · 8 hydrogen bonds · protein-protein
- G–H · 628 Ų buried · 9 hydrogen bonds · protein-protein
- A–G · 261 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4V0N · Crystal structure of BBS1N in complex with ARL6DN, soaked with mercury · the same entry in another collection · chain A against A, 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 A8JF99
- Every structure of UniProt A8JEA1
- Elsewhere: RCSB PDB 4V0N · PDBe 4V0N · UniProt A8JF99 · UniProt A8JEA1
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