MolNFT v1 · #126589 · protein
Human porphobilinogen deaminase in complex with dpm cofactor
5M7F: “Human porphobilinogen deaminase in complex with dpm cofactor”. X-ray diffraction, 2 ligands (DPM, SO4), 3 pockets (best druggability 0.69). MolNFT v1 #126589 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5M7F
- Type
- protein
- Length
- 633 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, SO4
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Porphobilinogen deaminase (EC 2.5.1.61) | protein | 317 | 36% helix, 24% strand | P08397 |
| B | Porphobilinogen deaminase (EC 2.5.1.61) | protein | 316 | 37% 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 A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
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 | 488 | 0.69 | 0.80 | 57 | DPM |
| 2 | 469 | 0.69 | 0.80 | 54 | DPM |
| 3 | 83 | 0.35 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 88 Ų buried · 1 hydrogen bond · 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 5M7F · PDBe 5M7F · UniProt P08397
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