MolNFT v1 · #106082 · protein
Crystal structure of the VAV2 SH2 domain in complex with txnip phosphorylated peptide
4ROJ · Guanine nucleotide exchange factor VAV2: “Crystal structure of the VAV2 SH2 domain in complex with txnip phosphorylated peptide”. X-ray diffraction, 2 ligands (UNX, NH2), 2 pockets (best druggability 0.63). MolNFT v1 #106082 on…
- PDB
- 4ROJ
- Type
- protein
- Length
- 331 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide exchange factor VAV2; Thioredoxin-interacting protein
- UniProt
- P52735, Q9H3M7
- Ligands
- UNX, NH2
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Guanine nucleotide exchange factor VAV2 | protein | 103 | 20% helix, 33% strand | P52735 |
| D | Thioredoxin-interacting protein | protein | 8 | 0% helix, 0% strand | Q9H3M7 |
| E, F | Thioredoxin-interacting protein | protein | 7 | 0% helix, 0% strand | Q9H3M7 |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · 14 copies · chains A, D, B, C, F
- NH2 · Amino group · ion · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 524 | 0.63 | 0.76 | 45 | UNX |
| 2 | 200 | 0.53 | 0.78 | 26 | empty |
Interfaces
7 interfaces between chains.
- B–E · 438 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 432 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 390 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 239 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 217 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified, 1 disulfide (phosphorylation, disulfide).
Compared structures
- 4ROJ · Crystal Structure of the VAV2 SH2 domain in complex with TXNIP phosphorylated peptide · the same entry in another collection · chain F against F, TM-score 1.00
- P52735 · AlphaFold monomer V2.0 prediction for guanine nucleotide exchange factor VAV2 (P52735) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9H3M7 · AlphaFold monomer V2.0 prediction for thioredoxin-interacting protein (Q9H3M7) · a predicted model of the same protein · chain E against A, TM-score 0.53
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 P52735
- Every structure of UniProt Q9H3M7
- Elsewhere: RCSB PDB 4ROJ · PDBe 4ROJ · UniProt P52735 · UniProt Q9H3M7
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