MolNFT v1 · #112227 · protein
Crystal structure of PFHAD1 in complex with glyceraldehyde-3-phosphate
4ZEX: “Crystal structure of PFHAD1 in complex with glyceraldehyde-3-phosphate”. X-ray diffraction, 3 ligands (G3H, MG, PO4), 8 pockets (best druggability 0.71). MolNFT v1 #112227 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4ZEX
- Type
- protein
- Length
- 560 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PFHAD1
- UniProt
- Q8IJ74
- Ligands
- G3H, MG, PO4
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PFHAD1 | protein | 290 | 40% helix, 22% strand | Q8IJ74 |
| B | PFHAD1 | protein | 270 | 43% helix, 21% strand | Q8IJ74 |
Ligands and binding sites
- G3H · Glyceraldehyde-3-phosphate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.71 | 0.98 | 21 | MG, G3H |
| 2 | 472 | 0.68 | 0.79 | 47 | MG, PO4 |
| 3 | 61 | 0.50 | 0.86 | 15 | empty |
| 4 | 167 | 0.44 | 0.75 | 25 | empty |
| 5 | 71 | 0.43 | 0.81 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 520 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4ZEX · Crystal structure of PfHAD1 in complex with glyceraldehyde-3-phosphate · the same entry in another collection · chain A against A, TM-score 1.00
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 Q8IJ74
- Elsewhere: RCSB PDB 4ZEX · PDBe 4ZEX · UniProt Q8IJ74
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