MolNFT v1 · #34409 · protein
Crystal structure of the SH3 domain of betapix in complex with a high affinity peptide from PAK2
2DF6 · Rho guanine nucleotide exchange factor 7: “Crystal structure of the SH3 domain of betapix in complex with a high affinity peptide from PAK2”. X-ray diffraction, 1 pocket (best druggability 0.48). MolNFT v1 #34409 on GenesisL1: 3D…
- PDB
- 2DF6
- Type
- protein
- Length
- 148 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rho guanine nucleotide exchange factor 7; 18-mer from PAK2
- EC
- 2.7.1.37
- UniProt
- O55043
- Pockets
- 1 · best druggability 0.48
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Rho guanine nucleotide exchange factor 7 | protein | 59 | 5% helix, 49% strand | O55043 |
| C | 18-mer from PAK2 (EC 2.7.1.37) | protein | 18 | 17% helix, 0% strand | — |
| D | 18-mer from PAK2 (EC 2.7.1.37) | protein | 12 | 25% helix, 0% strand | — |
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.48 | 0.82 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–C · 704 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 495 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 202 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 92 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 89 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2DF6 · Crystal Structure of the SH3 Domain of betaPIX in Complex with a High Affinity Peptide… · the same entry in another collection · chain A against A, TM-score 1.00
- O55043 · AlphaFold monomer V2.0 prediction for rho guanine nucleotide exchange factor 7 (O55043) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 O55043
- Elsewhere: RCSB PDB 2DF6 · PDBe 2DF6 · UniProt O55043
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