Research workbench
Crystal structure of ohya-PEG400 complex from staphylococcus aureus
Analyse Crystal structure of ohya-PEG400 complex from staphylococcus aureus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KAV
- Type
- protein
- Length
- 1,747 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oleate hydratase
- UniProt
- A0A0D6GJV1
- Ligands
- K
- Pockets
- 16 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Oleate hydratase | protein | 581 | 37% helix, 17% strand | A0A0D6GJV1 |
| A, C | Oleate hydratase | protein | 583 | 37% helix, 17% strand | A0A0D6GJV1 |
Ligands and binding sites
- K · Potassium ion · metal · 2 copies · chains B, A
- GOL · Glycerol · additive · 4 copies · chains B, A, C
- P6G · Hexaethylene glycol · additive · 3 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1017 | 0.86 | 0.87 | 104 | P6G, GOL |
| 2 | 1184 | 0.84 | 0.85 | 113 | P6G |
| 3 | 175 | 0.81 | 0.96 | 35 | P6G |
| 4 | 795 | 0.75 | 0.80 | 64 | empty |
| 5 | 69 | 0.73 | 0.98 | 26 | empty |
Interfaces
2 interfaces between chains.
- A–C · 2370 Ų buried · 38 hydrogen bonds · protein-protein
- B–A · 404 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7KAV · Crystal structure of OhyA-PEG400 complex from Staphylococcus aureus · 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 A0A0D6GJV1
- Elsewhere: RCSB PDB 7KAV · PDBe 7KAV · UniProt A0A0D6GJV1
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