Research workbench
Human porphobilinogen deaminase in complex with cofactor
Analyse Human porphobilinogen deaminase in complex with cofactor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AAJ
- Type
- protein
- Length
- 647 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Porphobilinogen deaminase
- EC
- 2.5.1.61
- UniProt
- P08397
- Ligands
- DPM
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Porphobilinogen deaminase (EC 2.5.1.61) | protein | 324 | 37% helix, 23% strand | P08397 |
| A | Porphobilinogen deaminase (EC 2.5.1.61) | protein | 323 | 34% helix, 23% strand | P08397 |
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 · 2 copies · chains B, A
- GOL · Glycerol · additive · 3 copies · chains B, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 582 | 0.71 | 0.79 | 63 | DPM |
| 2 | 399 | 0.69 | 0.81 | 52 | DPM |
| 3 | 54 | 0.29 | 0.75 | 9 | empty |
Interfaces
1 interface between chains.
- B–A · 16 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
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 P08397
- Elsewhere: RCSB PDB 7AAJ · PDBe 7AAJ · UniProt P08397
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