Research workbench
Crystal structure of lukgh from staphylococcus aureus in complex with a neutralising antibody
Analyse Crystal structure of lukgh from staphylococcus aureus in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K59
- Type
- protein
- Length
- 1,982 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized leukocidin-like protein 2; Uncharacterized leukocidin-like protein 1; Fab…
- UniProt
- Q2FFA2, Q2FFA3
- Ligands
- CL, PO4
- Pockets
- 19 · best druggability 0.72
Structure
x-ray diffraction · 7 distinct chains · 5% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Uncharacterized leukocidin-like protein 2 | protein | 275 | 4% helix, 60% strand | Q2FFA2 |
| B | Uncharacterized leukocidin-like protein 1 | protein | 293 | 4% helix, 58% strand | Q2FFA3 |
| C | Uncharacterized leukocidin-like protein 2 | protein | 276 | 4% helix, 59% strand | Q2FFA2 |
| A | Uncharacterized leukocidin-like protein 1 | protein | 292 | 4% helix, 57% strand | Q2FFA3 |
| H | Fab heavy chain | protein | 212 | 6% helix, 53% strand | — |
| L, F | Fab light chain | protein | 212 | 7% helix, 53% strand | — |
| E | Fab heavy chain | protein | 210 | 6% helix, 51% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · chains D, B
- PO4 · Phosphate ion · ion · chains A
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1083 | 0.72 | 0.76 | 109 | empty |
| 2 | 675 | 0.63 | 0.74 | 61 | empty |
| 3 | 524 | 0.63 | 0.76 | 60 | empty |
| 4 | 171 | 0.61 | 0.84 | 31 | empty |
| 5 | 163 | 0.60 | 0.84 | 29 | empty |
Interfaces
10 interfaces between chains.
- C–A · 2249 Ų buried · 52 hydrogen bonds · protein-protein
- D–B · 2242 Ų buried · 50 hydrogen bonds · protein-protein
- H–L · 1709 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1691 Ų buried · 18 hydrogen bonds · protein-protein
- H–E · 594 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5K59 · Crystal structure of LukGH from Staphylococcus aureus in complex with a neutralising… · the same entry in another collection · chain F against F, TM-score 1.00
- Q2FFA2 · AlphaFold monomer V2.0 prediction for uncharacterized leukocidin-like protein 2 (Q2FFA2) · a predicted model of the same protein · chain D against A, TM-score 0.98
- Q2FFA3 · AlphaFold monomer V2.0 prediction for uncharacterized leukocidin-like protein 1 (Q2FFA3) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q2FFA2
- Every structure of UniProt Q2FFA3
- Elsewhere: RCSB PDB 5K59 · PDBe 5K59 · UniProt Q2FFA2 · UniProt Q2FFA3
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