MolNFT v1 · #34421 · protein
Crystal structure of the CDC42-collybistin II complex
2DFK: “Crystal structure of the CDC42-collybistin II complex”. X-ray diffraction, 1 ligand (SO4), 14 pockets (best druggability 0.69). MolNFT v1 #34421 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2DFK
- Type
- protein
- Length
- 1,094 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Collybistin II; Cell division cycle 42 isoform 1
- UniProt
- Q9QX73, P60953
- Ligands
- SO4
- Pockets
- 14 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Collybistin II | protein | 365 | 57% helix, 15% strand | Q9QX73 |
| B | Cell division cycle 42 isoform 1 | protein | 187 | 36% helix, 21% strand | P60953 |
| C | Collybistin II | protein | 353 | 58% helix, 15% strand | Q9QX73 |
| D | Cell division cycle 42 isoform 1 | protein | 189 | 37% helix, 20% strand | P60953 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains B, D
- GOL · Glycerol · additive · 6 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 787 | 0.69 | 0.76 | 65 | SO4 |
| 2 | 304 | 0.68 | 0.83 | 35 | empty |
| 3 | 106 | 0.66 | 0.90 | 26 | empty |
| 4 | 394 | 0.65 | 0.79 | 39 | empty |
| 5 | 215 | 0.55 | 0.78 | 25 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1732 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1568 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 821 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 786 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2DFK · Crystal structure of the CDC42-Collybistin II complex · the same entry in another collection · chain D against D, TM-score 1.00
- Q9QX73 · AlphaFold monomer V2.0 prediction for rho guanine nucleotide exchange factor 9 (Q9QX73) · a predicted model of the same protein · chain C against A, TM-score 0.97
- P60953 · AlphaFold monomer V2.0 prediction for cell division control protein 42 homolog (P60953) · a predicted model of the same protein · chain B against A, TM-score 0.89
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 Q9QX73
- Every structure of UniProt P60953
- Elsewhere: RCSB PDB 2DFK · PDBe 2DFK · UniProt Q9QX73 · UniProt P60953
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