MolNFT v1 · #13041 · protein
DBSCDC42(Y889F)
1KZG · Guanine nucleotide exchange factor dbs: “DBSCDC42(Y889F)”. X-ray diffraction, 11 pockets (best druggability 0.70). MolNFT v1 #13041 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1KZG
- Type
- protein
- Length
- 1,032 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide exchange factor dbs; CDC42 homolog
- UniProt
- Q64096, P60953
- Pockets
- 11 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide exchange factor dbs | protein | 337 | 57% helix, 17% strand | Q64096 |
| B | CDC42 homolog | protein | 188 | 36% helix, 21% strand | P60953 |
| C | Guanine nucleotide exchange factor dbs | protein | 330 | 56% helix, 16% strand | Q64096 |
| D | CDC42 homolog | protein | 177 | 37% helix, 22% strand | P60953 |
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 719 | 0.70 | 0.77 | 80 | empty |
| 2 | 582 | 0.67 | 0.77 | 62 | empty |
| 3 | 271 | 0.53 | 0.75 | 34 | empty |
| 4 | 164 | 0.51 | 0.78 | 26 | empty |
| 5 | 144 | 0.50 | 0.79 | 22 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1721 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1676 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1062 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1KZG · DbsCdc42(Y889F) · the same entry in another collection · chain D against D, TM-score 1.00
- Q64096 · AlphaFold monomer V2.0 prediction for guanine nucleotide exchange factor dbs (Q64096) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P60953 · AlphaFold monomer V2.0 prediction for cell division control protein 42 homolog (P60953) · a predicted model of the same protein · chain D against A, TM-score 0.93
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 Q64096
- Every structure of UniProt P60953
- Elsewhere: RCSB PDB 1KZG · PDBe 1KZG · UniProt Q64096 · UniProt P60953
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