MolNFT v1 · #20576 · protein
Crystal structure of the DH/PH fragment of dbs without bound GTPase
1RJ2 · Guanine nucleotide exchange factor dbs [fragment]: “Crystal structure of the DH/PH fragment of dbs without bound GTPase”. X-ray diffraction, 12 pockets (best druggability 0.70). MolNFT v1 #20576 on GenesisL1: 3D structure, binding…
- PDB
- 1RJ2
- Type
- protein
- Length
- 1,273 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide exchange factor dbs [fragment]
- UniProt
- Q63406
- Pockets
- 12 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide exchange factor dbs [fragment] | protein | 317 | 56% helix, 14% strand | Q63406 |
| D | Guanine nucleotide exchange factor dbs [fragment] | protein | 331 | 51% helix, 15% strand | Q63406 |
| G | Guanine nucleotide exchange factor dbs [fragment] | protein | 307 | 55% helix, 10% strand | Q63406 |
| J | Guanine nucleotide exchange factor dbs [fragment] | protein | 318 | 53% helix, 12% strand | Q63406 |
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.70 | 0.89 | 24 | empty |
| 2 | 424 | 0.61 | 0.76 | 45 | empty |
| 3 | 312 | 0.58 | 0.77 | 49 | empty |
| 4 | 301 | 0.54 | 0.75 | 39 | empty |
| 5 | 165 | 0.45 | 0.75 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–D · 785 Ų buried · 14 hydrogen bonds · protein-protein
- G–J · 656 Ų buried · 11 hydrogen bonds · protein-protein
- D–G · 554 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1RJ2 · Crystal structure of the DH/PH fragment of Dbs without bound GTPase · the same entry in another collection · chain J against J, TM-score 1.00
- Q63406 · AlphaFold monomer V2.0 prediction for guanine nucleotide exchange factor dbs (Q63406) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q63406
- Elsewhere: RCSB PDB 1RJ2 · PDBe 1RJ2 · UniProt Q63406
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