Research workbench
Crystal structure of human FMNL2 gbd-FH3 domains bound to CDC42-gppnhp
Analyse Crystal structure of human FMNL2 gbd-FH3 domains bound to CDC42-gppnhp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YC7
- Type
- protein
- Length
- 470 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formin-like protein 2; Cell division control protein 42 homolog
- UniProt
- Q96PY5, P60953
- Ligands
- GNP, MG
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 61% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Formin-like protein 2 | protein | 291 | 74% helix, 0% strand | Q96PY5 |
| A | Cell division control protein 42 homolog | protein | 179 | 40% helix, 25% strand | P60953 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 410 | 0.65 | 0.79 | 51 | empty |
| 2 | 158 | 0.53 | 0.79 | 32 | GNP, MG |
| 3 | 118 | 0.49 | 0.80 | 17 | empty |
| 4 | 50 | 0.24 | 0.72 | 11 | empty |
Interfaces
1 interface between chains.
- B–A · 1664 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 4YC7 · Crystal structure of human FMNL2 GBD-FH3 Domains bound to Cdc42-GppNHp · the same entry in another collection · chain B against B, TM-score 1.00
- Q96PY5 · AlphaFold monomer V2.0 prediction for formin-like protein 2 (Q96PY5) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P60953 · AlphaFold monomer V2.0 prediction for cell division control protein 42 homolog (P60953) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q96PY5
- Every structure of UniProt P60953
- Elsewhere: RCSB PDB 4YC7 · PDBe 4YC7 · UniProt Q96PY5 · UniProt P60953
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