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Crystal structure of the 2-iodoporphobilinogen-bound ES2 intermediate form of human hydroxymethylbilane synthase
Analyse Crystal structure of the 2-iodoporphobilinogen-bound ES2 intermediate form of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CD0
- Type
- protein
- Length
- 643 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.31
- Source
- Homo sapiens
- Molecule
- Porphobilinogen deaminase
- EC
- 2.5.1.61
- UniProt
- P08397
- Ligands
- 7J8, FWL
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · resolution 2.31 · 2 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Porphobilinogen deaminase (EC 2.5.1.61) | protein | 323 | 37% helix, 24% strand | P08397 |
| B | Porphobilinogen deaminase (EC 2.5.1.61) | protein | 320 | 36% helix, 24% strand | P08397 |
Ligands and binding sites
- 7J8 · 3-[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-3-(3-hydroxy-3-oxopropyl)-5-methyl-1~{H}-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-1~{H}-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-1~{H}-pyrrol-2-yl]methyl]-1~{H}-pyrrol-3-yl]propanoic acid · ligand · 2 copies · chains A, B
- FWL · 3-[5-(aminomethyl)-4-(carboxymethyl)-2-iodo-1H-pyrrol-3-yl]propanoic acid · ligand · chains 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 738 | 0.73 | 0.79 | 59 | 7J8 |
| 2 | 609 | 0.72 | 0.79 | 60 | 7J8, FWL |
| 3 | 322 | 0.60 | 0.78 | 37 | empty |
| 4 | 139 | 0.53 | 0.81 | 25 | empty |
| 5 | 92 | 0.47 | 0.81 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1014 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7CD0 · Crystal structure of the 2-iodoporphobilinogen-bound ES2 intermediate form of human… · 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 B against A, TM-score 0.97
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 7CD0 · PDBe 7CD0 · UniProt P08397
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