Research workbench
Crystal structure of vav and GRB2 SH3 domains
Analyse Crystal structure of vav and GRB2 SH3 domains in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GCQ
- Type
- protein
- Length
- 182 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Growth factor receptor-bound protein 2; Vav proto-oncogene
- UniProt
- P62993, P27870
- Pockets
- 2 · best druggability 0.39
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Growth factor receptor-bound protein 2 | protein | 56 | 5% helix, 52% strand | P62993 |
| B | Growth factor receptor-bound protein 2 | protein | 57 | 5% helix, 49% strand | P62993 |
| C | Vav proto-oncogene | protein | 69 | 9% helix, 41% strand | P27870 |
Ligands and binding sites
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.39 | 0.77 | 19 | empty |
| 2 | 72 | 0.38 | 0.78 | 17 | empty |
Interfaces
2 interfaces between chains.
- B–C · 628 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 456 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1GCQ · Crystal structure of vav and GRB2 SH3 domains · the same entry in another collection · chain A against A, TM-score 1.00
- P62993 · AlphaFold monomer V2.0 prediction for growth factor receptor-bound protein 2 (P62993) · a predicted model of the same protein · chain A against A, TM-score 0.96
- P27870 · AlphaFold monomer V2.0 prediction for proto-oncogene vav (P27870) · a predicted model of the same protein · chain C 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 P62993
- Every structure of UniProt P27870
- Elsewhere: RCSB PDB 1GCQ · PDBe 1GCQ · UniProt P62993 · UniProt P27870
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