Research workbench
Crystal structure of the holo form of human hydroxymethylbilane synthase
Analyse Crystal structure of the holo form of human hydroxymethylbilane synthase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CCX
- Type
- protein
- Length
- 627 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 0.76
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Porphobilinogen deaminase (EC 2.5.1.61) | protein | 318 | 37% helix, 25% strand | P08397 |
| C | Porphobilinogen deaminase (EC 2.5.1.61) | protein | 309 | 39% helix, 25% 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 A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 609 | 0.76 | 0.82 | 71 | empty |
| 2 | 252 | 0.69 | 0.85 | 50 | DPM |
| 3 | 328 | 0.63 | 0.79 | 46 | DPM |
Interfaces
1 interface between chains.
- A–C · 432 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7CCX · Crystal structure of the holo form of human hydroxymethylbilane synthase · the same entry in another collection · chain A against A, TM-score 1.00
- P08397 · AlphaFold monomer V2.0 prediction for porphobilinogen deaminase (P08397) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 7CCX · PDBe 7CCX · UniProt P08397
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