Research workbench
Porphobilinogen deaminase from arabidopsis thaliana
Analyse Porphobilinogen deaminase from arabidopsis thaliana in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HTG
- Type
- protein
- Length
- 302 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Porphobilinogen deaminase, chloroplastic
- EC
- 2.5.1.61
- UniProt
- Q43316
- Ligands
- 18W
- Pockets
- 3 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Porphobilinogen deaminase, chloroplastic (EC 2.5.1.61) | protein | 302 | 36% helix, 24% strand | Q43316 |
Ligands and binding sites
- 18W · 3-[(5Z)-5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methylidene}-4-(carboxymethyl)-2-oxo-2,5-dihydro-1H-pyrrol-3-yl]propanoic acid · ligand · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 530 | 0.85 | 0.91 | 71 | 18W, ACT |
| 2 | 103 | 0.42 | 0.77 | 16 | empty |
| 3 | 52 | 0.28 | 0.75 | 13 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4HTG · Porphobilinogen Deaminase from Arabidopsis Thaliana · the same entry in another collection · chain A against A, TM-score 1.00
- Q43316 · AlphaFold monomer V2.0 prediction for porphobilinogen deaminase, chloroplastic (Q43316) · a predicted model of the same protein · 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 Q43316
- Elsewhere: RCSB PDB 4HTG · PDBe 4HTG · UniProt Q43316
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