Research workbench
Structural basis of promiscuous guanine nucleotide exchange by the T-cell essential VAV1
Analyse Structural basis of promiscuous guanine nucleotide exchange by the T-cell… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BJI
- Type
- protein
- Length
- 1,081 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proto-oncogene vav; RAS-related C3 botulinum toxin substrate 1 precursor
- UniProt
- P15498, P63000
- Ligands
- ZN
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene vav | protein | 372 | 54% helix, 16% strand | P15498 |
| B | Proto-oncogene vav | protein | 368 | 52% helix, 17% strand | P15498 |
| C | RAS-related C3 botulinum toxin substrate 1 precursor | protein | 177 | 36% helix, 22% strand | P63000 |
| D | RAS-related C3 botulinum toxin substrate 1 precursor | protein | 164 | 32% helix, 21% strand | P63000 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 968 | 0.86 | 0.87 | 79 | empty |
| 2 | 218 | 0.60 | 0.81 | 34 | empty |
| 3 | 274 | 0.59 | 0.79 | 35 | empty |
| 4 | 343 | 0.58 | 0.76 | 44 | empty |
| 5 | 316 | 0.58 | 0.77 | 41 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1370 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 1286 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 311 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 220 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 123 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3BJI · Structural Basis of Promiscuous Guanine Nucleotide Exchange by the T-Cell Essential Vav1 · the same entry in another collection · chain A against A, TM-score 1.00
- P15498 · AlphaFold monomer V2.0 prediction for proto-oncogene vav (P15498) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P15498
- Every structure of UniProt P63000
- Elsewhere: RCSB PDB 3BJI · PDBe 3BJI · UniProt P15498 · UniProt P63000
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