Research workbench
Pplo at 1.23 ångströms
Analyse Pplo at 1.23 ångströms in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1W7C
- Type
- protein
- Length
- 737 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysyl oxidase
- EC
- 1.4.3.13
- UniProt
- Q96X16
- Ligands
- NAG, BMA, MG, CA, CU, CL
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysyl oxidase (EC 1.4.3.13) | protein | 737 | 14% helix, 39% strand | Q96X16 |
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 · 5 copies · chains A
- CA · Calcium ion · metal · 2 copies · chains A
- CU · Copper (II) ion · metal · chains A
- CL · Chloride ion · ion · 5 copies · chains A
- IMD · Imidazole · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.77 | 0.96 | 31 | empty |
| 2 | 498 | 0.65 | 0.77 | 59 | IMD |
| 3 | 234 | 0.55 | 0.78 | 24 | empty |
| 4 | 168 | 0.45 | 0.75 | 23 | empty |
| 5 | 64 | 0.37 | 0.79 | 18 | empty |
Modifications
Observed in the structure: 5 glycan, 3 disulfide, 1 modified (N-glycosylation, disulfide, nonstandard).
Compared structures
- 1W7C · PPLO at 1.23 Angstroms · 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
- Every structure of UniProt Q96X16
- Elsewhere: RCSB PDB 1W7C · PDBe 1W7C · UniProt Q96X16
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