MolNFT v1 · #141631 · protein
Crystal structure of human lysyl oxidase-like 2 (HLOXL2) in a precursor state
5ZE3 · Lysyl oxidase homolog 2: “Crystal structure of human lysyl oxidase-like 2 (HLOXL2) in a precursor state”. X-ray diffraction, 4 ligands (NAG, CA, ZN), 11 pockets (best druggability 0.74). MolNFT v1 #141631 on GenesisL1: 3D structure…
- PDB
- 5ZE3
- Type
- protein
- Length
- 884 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysyl oxidase homolog 2
- EC
- 1.4.3.13
- UniProt
- Q9Y4K0
- Ligands
- NAG, CA, ZN, SO4
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysyl oxidase homolog 2 (EC 1.4.3.13) | protein | 441 | 12% helix, 34% strand | Q9Y4K0 |
| B | Lysyl oxidase homolog 2 (EC 1.4.3.13) | protein | 443 | 12% helix, 33% strand | Q9Y4K0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.74 | 0.92 | 28 | SO4 |
| 2 | 549 | 0.71 | 0.80 | 43 | empty |
| 3 | 443 | 0.70 | 0.81 | 39 | empty |
| 4 | 125 | 0.63 | 0.87 | 30 | empty |
| 5 | 183 | 0.59 | 0.81 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1482 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5ZE3 · Crystal structure of human lysyl oxidase-like 2 (hLOXL2) in a precursor state · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y4K0 · AlphaFold monomer V2.0 prediction for lysyl oxidase homolog 2 (Q9Y4K0) · a predicted model of the same protein · chain A 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 Q9Y4K0
- Elsewhere: RCSB PDB 5ZE3 · PDBe 5ZE3 · UniProt Q9Y4K0
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