MolNFT v1 · #18074 · protein
Structure of porphobilinogen deaminase reveals a flexible multidomain polymerase with a single catalytic site
1PDA: “Structure of porphobilinogen deaminase reveals a flexible multidomain polymerase with a single catalytic site”. X-ray diffraction, 1 ligand (DPM), 2 pockets (best druggability 0.80). MolNFT v1 #18074 on GenesisL1: 3D structure…
- PDB
- 1PDA
- Type
- protein
- Length
- 296 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Porphobilinogen deaminase
- EC
- 2.5.1.61
- UniProt
- P06983
- Ligands
- DPM
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Porphobilinogen deaminase (EC 2.5.1.61) | protein | 296 | 38% helix, 24% strand | P06983 |
Ligands and binding sites
- DPM · 3-[5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid · ligand · chains A
- ACY · Acetic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 558 | 0.80 | 0.86 | 64 | DPM, ACY |
| 2 | 61 | 0.26 | 0.72 | 14 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1PDA · Structure of porphobilinogen deaminase reveals a flexible multidomain polymerase with a… · the same entry in another collection · chain A against A, TM-score 1.00
- P06983 · AlphaFold monomer V2.0 prediction for porphobilinogen deaminase (P06983) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P06983
- Elsewhere: RCSB PDB 1PDA · PDBe 1PDA · UniProt P06983
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