Research workbench
Crystal structure of porphobilinogen synthase complexed with the inhibitor 4,7-dioxosebacic acid
Analyse Crystal structure of porphobilinogen synthase complexed with the inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1L6S
- Type
- protein
- Length
- 646 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Porphobilinogen synthase
- EC
- 4.2.1.24
- UniProt
- P0ACB2
- Ligands
- DSB, ZN, MG
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Porphobilinogen synthase (EC 4.2.1.24) | protein | 323 | 41% helix, 17% strand | P0ACB2 |
Ligands and binding sites
- DSB · 4,7-dioxosebacic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 176 | 0.84 | 0.98 | 27 | empty |
| 2 | 134 | 0.64 | 0.86 | 17 | empty |
| 3 | 114 | 0.62 | 0.87 | 16 | empty |
| 4 | 355 | 0.60 | 0.77 | 49 | empty |
| 5 | 357 | 0.59 | 0.76 | 46 | empty |
Interfaces
1 interface between chains.
- A–B · 3241 Ų buried · 71 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 2 modified (covalent ligand, artifact).
Compared structures
- 1L6S · Crystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
- P0ACB2 · AlphaFold monomer V2.0 prediction for delta-aminolevulinic acid dehydratase (P0ACB2) · 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 P0ACB2
- Elsewhere: RCSB PDB 1L6S · PDBe 1L6S · UniProt P0ACB2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.