MolNFT v1 · #58965 · protein
Crystal structure of putative 3-oxoacyl-(acyl-carrier-protein) synthase from pseudomonas aeruginosa
3BJD: “Crystal structure of putative 3-oxoacyl-(acyl-carrier-protein) synthase from pseudomonas aeruginosa”. X-ray diffraction, 1 ligand (NI), 14 pockets (best druggability 0.88). MolNFT v1 #58965 on GenesisL1: 3D structure, binding sites…
- PDB
- 3BJD
- Type
- protein
- Length
- 967 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative 3-oxoacyl-(acyl-carrier-protein) synthase
- UniProt
- Q9HY91
- Ligands
- NI
- Pockets
- 14 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative 3-oxoacyl-(acyl-carrier-protein) synthase | protein | 321 | 73% helix, 0% strand | Q9HY91 |
| B | Putative 3-oxoacyl-(acyl-carrier-protein) synthase | protein | 322 | 72% helix, 0% strand | Q9HY91 |
| C | Putative 3-oxoacyl-(acyl-carrier-protein) synthase | protein | 324 | 71% helix, 0% strand | Q9HY91 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 693 | 0.88 | 0.92 | 94 | EDO |
| 2 | 451 | 0.80 | 0.88 | 60 | empty |
| 3 | 447 | 0.77 | 0.86 | 54 | empty |
| 4 | 607 | 0.77 | 0.83 | 52 | EDO |
| 5 | 587 | 0.72 | 0.80 | 49 | EDO |
Interfaces
3 interfaces between chains.
- A–B · 1873 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 277 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 244 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3BJD · Crystal structure of putative 3-oxoacyl-(acyl-carrier-protein) synthase from Pseudomonas… · the same entry in another collection · chain B against B, 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 Q9HY91
- Elsewhere: RCSB PDB 3BJD · PDBe 3BJD · UniProt Q9HY91
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