Research workbench
PPLO + XE
Analyse PPLO + XE in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RKY
- Type
- protein
- Length
- 735 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysyl oxidase
- EC
- 1.4.3.13
- Ligands
- NAG, BMA, MG, CA, CU, XE, CL
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysyl oxidase (EC 1.4.3.13) | protein | 735 | 14% helix, 40% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- MG · Magnesium ion · metal · 3 copies · chains A
- CA · Calcium ion · metal · 2 copies · chains A
- CU · Copper (II) ion · metal · chains A
- XE · Xenon · ion · 8 copies · chains A
- CL · Chloride ion · ion · 6 copies · chains A
- IMD · Imidazole · additive · chains A
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 | 82 | 0.73 | 0.97 | 17 | empty |
| 2 | 512 | 0.65 | 0.77 | 65 | IMD |
| 3 | 237 | 0.56 | 0.78 | 22 | empty |
| 4 | 162 | 0.45 | 0.76 | 21 | empty |
| 5 | 51 | 0.43 | 0.84 | 18 | empty |
Modifications
Observed in the structure: 5 glycan, 3 disulfide, 1 modified (N-glycosylation, disulfide, nonstandard).
Compared structures
- 1RKY · PPLO + Xe · 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
- Elsewhere: RCSB PDB 1RKY · PDBe 1RKY
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