MolNFT v1 · #13291 · protein
Crystal structure of porphobilinogen synthase complexed with the inhibitor 4-oxosebacic acid
1L6Y: “Crystal structure of porphobilinogen synthase complexed with the inhibitor 4-oxosebacic acid”. X-ray diffraction, 3 ligands (4OX, ZN, MG), 6 pockets (best druggability 0.82). MolNFT v1 #13291 on GenesisL1: 3D structure, binding…
- PDB
- 1L6Y
- 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
- 4OX, ZN, MG
- Pockets
- 6 · best druggability 0.82
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
- 4OX · 4-oxodecanedioic 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
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 138 | 0.82 | 0.99 | 25 | empty |
| 2 | 400 | 0.66 | 0.79 | 50 | ZN, 4OX |
| 3 | 359 | 0.64 | 0.79 | 50 | ZN, 4OX |
| 4 | 138 | 0.61 | 0.85 | 20 | empty |
| 5 | 136 | 0.57 | 0.83 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 3218 Ų buried · 68 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, artifact).
Compared structures
- 1L6Y · Crystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor 4-Oxosebacic… · 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 1L6Y · PDBe 1L6Y · UniProt P0ACB2
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