Research workbench
Human ykl-39 is a pseudo-chitinase with retained chitooligosaccharide binding properties
Analyse Human ykl-39 is a pseudo-chitinase with retained chitooligosaccharide binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AY1
- Type
- protein
- Length
- 4,368 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chitinase-3-like protein 2
- UniProt
- Q15782
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Chitinase-3-like protein 2 | protein | 364 | 37% helix, 24% strand | Q15782 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 48 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1128 | 0.78 | 0.80 | 99 | empty |
| 2 | 1109 | 0.76 | 0.79 | 95 | empty |
| 3 | 649 | 0.76 | 0.81 | 69 | NAG |
| 4 | 1195 | 0.73 | 0.76 | 118 | NAG |
| 5 | 1168 | 0.73 | 0.76 | 119 | empty |
Interfaces
24 interfaces between chains.
- B–L · 771 Ų buried · 10 hydrogen bonds · protein-protein
- A–G · 767 Ų buried · 8 hydrogen bonds · protein-protein
- C–L · 541 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 470 Ų buried · 1 hydrogen bond · protein-protein
- A–H · 421 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 4AY1 · Human YKL-39 is a pseudo-chitinase with retained chitooligosaccharide binding properties · the same entry in another collection · chain L against L, 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 Q15782
- Elsewhere: RCSB PDB 4AY1 · PDBe 4AY1 · UniProt Q15782
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