MolNFT v1 · #73750 · protein
Crystal structure of delta-aminolevulinic acid dehydratase (porphobilinogen synthase) from toxoplasma gondii ME49 in complex with the reaction product porphobilinogen
3OBK: “Crystal structure of delta-aminolevulinic acid dehydratase (porphobilinogen synthase) from toxoplasma gondii…”. X-ray diffraction, 3 ligands (PBG, MG, CL), 20 pockets (best druggability 0.86). MolNFT v1 #73750 on GenesisL1: 3D…
- PDB
- 3OBK
- Type
- protein
- Length
- 2,816 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Delta-aminolevulinic acid dehydratase
- EC
- 4.2.1.24
- UniProt
- B6KNM2
- Ligands
- PBG, MG, CL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Delta-aminolevulinic acid dehydratase (EC 4.2.1.24) | protein | 352 | 43% helix, 18% strand | B6KNM2 |
Ligands and binding sites
- PBG · 3-[5-(aminomethyl)-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- CL · Chloride ion · ion · 16 copies · chains C, A, B, E, D, H, F, G
- EDO · 1,2-ethanediol · additive · 19 copies · chains A, C, B, E, D, H, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1188 | 0.86 | 0.87 | 120 | EDO |
| 2 | 54 | 0.74 | 0.99 | 17 | EDO |
| 3 | 57 | 0.72 | 0.98 | 21 | PBG |
| 4 | 50 | 0.72 | 0.99 | 20 | PBG |
| 5 | 385 | 0.71 | 0.83 | 45 | CL, EDO |
Interfaces
16 interfaces between chains.
- A–B · 3697 Ų buried · 79 hydrogen bonds · protein-protein
- E–F · 3688 Ų buried · 79 hydrogen bonds · protein-protein
- C–D · 3673 Ų buried · 82 hydrogen bonds · protein-protein
- G–H · 3660 Ų buried · 73 hydrogen bonds · protein-protein
- F–G · 3188 Ų buried · 65 hydrogen bonds · protein-protein
Compared structures
- 3OBK · Crystal structure of delta-aminolevulinic acid dehydratase (porphobilinogen synthase)… · the same entry in another collection · 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 B6KNM2
- Elsewhere: RCSB PDB 3OBK · PDBe 3OBK · UniProt B6KNM2
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