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Crystal Structure of LysM domain from pteris ryukyuensis chitinase A
Analyse Crystal Structure of LysM domain from pteris ryukyuensis chitinase A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YLG
- Type
- protein
- Length
- 188 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.48
- Source
- Pteris ryukyuensis
- Molecule
- Chitinase A
- UniProt
- Q0WYK2
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.33
Structure
x-ray diffraction · resolution 1.48 · 4 distinct chains · 36% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chitinase A | protein | 47 | 36% helix, 13% strand | Q0WYK2 |
| B | Chitinase A | protein | 47 | 38% helix, 13% strand | Q0WYK2 |
| C | Chitinase A | protein | 46 | 30% helix, 13% strand | Q0WYK2 |
| D | Chitinase A | protein | 48 | 38% helix, 13% strand | Q0WYK2 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.33 | 0.72 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–D · 357 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 338 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 320 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 160 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 150 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5YLG · Crystal structure of lysm domain from pteris ryukyuensis chitinase a · 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 Q0WYK2
- Elsewhere: RCSB PDB 5YLG · PDBe 5YLG · UniProt Q0WYK2
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