MolNFT v1 · #20391 · protein
G50P mutant of phosphonoacetaldehyde hydrolase in complex with substrate analogue vinyl sulfonate
1RDF: “G50P mutant of phosphonoacetaldehyde hydrolase in complex with substrate analogue vinyl sulfonate”. X-ray diffraction, 2 ligands (ESA, MG), 17 pockets (best druggability 0.73). MolNFT v1 #20391 on GenesisL1: 3D structure, binding…
- PDB
- 1RDF
- Type
- protein
- Length
- 1,578 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphonoacetaldehyde hydrolase
- UniProt
- O31156
- Ligands
- ESA, MG
- Pockets
- 17 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Phosphonoacetaldehyde hydrolase | protein | 263 | 44% helix, 9% strand | O31156 |
Ligands and binding sites
- ESA · Ethanesulfonic acid · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.73 | 0.95 | 26 | MG, ESA |
| 2 | 583 | 0.73 | 0.81 | 41 | empty |
| 3 | 55 | 0.70 | 0.98 | 16 | MG, ESA |
| 4 | 450 | 0.69 | 0.80 | 62 | empty |
| 5 | 249 | 0.64 | 0.82 | 35 | MG, ESA |
Interfaces
6 interfaces between chains.
- B–D · 872 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 823 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 270 Ų buried · 0 hydrogen bonds · protein-protein
- B–E · 126 Ų buried · 0 hydrogen bonds · protein-protein
- E–F · 44 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1RDF · G50P mutant of phosphonoacetaldehyde hydrolase in complex with substrate analogue vinyl… · the same entry in another collection · chain C against C, TM-score 1.00
- O31156 · AlphaFold monomer V2.0 prediction for phosphonoacetaldehyde hydrolase (O31156) · a predicted model of the same protein · chain A against A, TM-score 0.85
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 O31156
- Elsewhere: RCSB PDB 1RDF · PDBe 1RDF · UniProt O31156
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