MolNFT v1 · #18631 · protein
Crystal structure of a low activity F12L mutant of human porphobilinogen synthase
1PV8 · Delta-aminolevulinic acid dehydratase: “Crystal structure of a low activity F12L mutant of human porphobilinogen synthase”. X-ray diffraction, 2 ligands (PB1, ZN), 4 pockets (best druggability 0.47). MolNFT v1 #18631 on GenesisL1…
- PDB
- 1PV8
- Type
- protein
- Length
- 556 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Delta-aminolevulinic acid dehydratase
- EC
- 4.2.1.24
- UniProt
- P13716
- Ligands
- PB1, ZN
- Pockets
- 4 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Delta-aminolevulinic acid dehydratase (EC 4.2.1.24) | protein | 276 | 49% helix, 17% strand | P13716 |
| B | Delta-aminolevulinic acid dehydratase (EC 4.2.1.24) | protein | 280 | 47% helix, 18% strand | P13716 |
Ligands and binding sites
- PB1 · 3-(2-aminoethyl)-4-(aminomethyl)heptanedioic acid · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 167 | 0.47 | 0.76 | 30 | ZN, PB1 |
| 2 | 113 | 0.38 | 0.74 | 23 | empty |
| 3 | 84 | 0.36 | 0.76 | 22 | empty |
| 4 | 61 | 0.26 | 0.72 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1426 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1PV8 · Crystal structure of a low activity F12L mutant of human porphobilinogen synthase · the same entry in another collection · chain A against A, TM-score 1.00
- P13716 · AlphaFold monomer V2.0 prediction for delta-aminolevulinic acid dehydratase (P13716) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P13716
- Elsewhere: RCSB PDB 1PV8 · PDBe 1PV8 · UniProt P13716
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