MolNFT v1 · #143546 · protein
Crystal structure of xanthomonas campestris olea H285D
6B2T · 3-oxoacyl-[acp] synthase III: “Crystal structure of xanthomonas campestris olea H285D”. X-ray diffraction, 1 ligand (PO4), 3 pockets (best druggability 0.85). MolNFT v1 #143546 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6B2T
- Type
- protein
- Length
- 684 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-oxoacyl-[acp] synthase III
- EC
- 2.3.1.41
- UniProt
- Q8PDX2
- Ligands
- PO4
- Pockets
- 3 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-oxoacyl-[acp] synthase III (EC 2.3.1.41) | protein | 345 | 43% helix, 25% strand | Q8PDX2 |
| B | 3-oxoacyl-[acp] synthase III (EC 2.3.1.41) | protein | 339 | 42% helix, 25% strand | Q8PDX2 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 5 copies · chains A, B
- GOL · Glycerol · additive · 3 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1010 | 0.85 | 0.86 | 125 | PO4 |
| 2 | 221 | 0.67 | 0.84 | 39 | GOL |
| 3 | 196 | 0.61 | 0.82 | 41 | GOL |
Interfaces
1 interface between chains.
- A–B · 2409 Ų buried · 47 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 6B2T · Crystal structure of Xanthomonas campestris OleA H285D · the same entry in another collection · chain A against A, TM-score 1.00
- Q8PDX2 · AlphaFold monomer V2.0 prediction for acyl-COA:ACYL-CoA alkyltransferase (Q8PDX2) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q8PDX2
- Elsewhere: RCSB PDB 6B2T · PDBe 6B2T · UniProt Q8PDX2
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