MolNFT v1 · #65871 · protein
Crystal structure of putative triphosphoribosyl-dephospho-CoA synthase from archaeoglobus fulgidus
3H9P: “Crystal structure of putative triphosphoribosyl-dephospho-CoA synthase from archaeoglobus fulgidus”. X-ray diffraction, 1 ligand (CL), 7 pockets (best druggability 0.79). MolNFT v1 #65871 on GenesisL1: 3D structure, binding sites…
- PDB
- 3H9P
- Type
- protein
- Length
- 665 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative triphosphoribosyl-dephospho-CoA synthase
- UniProt
- O28441
- Ligands
- CL
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative triphosphoribosyl-dephospho-CoA synthase | protein | 226 | 75% helix, 0% strand | O28441 |
| B | Putative triphosphoribosyl-dephospho-CoA synthase | protein | 221 | 77% helix, 0% strand | O28441 |
| C | Putative triphosphoribosyl-dephospho-CoA synthase | protein | 218 | 77% helix, 0% strand | O28441 |
Ligands and binding sites
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1167 | 0.79 | 0.80 | 72 | empty |
| 2 | 392 | 0.61 | 0.76 | 39 | empty |
| 3 | 239 | 0.53 | 0.76 | 30 | empty |
| 4 | 151 | 0.45 | 0.75 | 21 | empty |
| 5 | 174 | 0.44 | 0.74 | 28 | empty |
Interfaces
2 interfaces between chains.
- A–B · 985 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 223 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 3H9P · Crystal structure of putative triphosphoribosyl-dephospho-coA synthase from Archaeoglobus… · 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 O28441
- Elsewhere: RCSB PDB 3H9P · PDBe 3H9P · UniProt O28441
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