Research workbench
Crystal structure of the catalytic domain of chitiniphilus shinanonensis chitinase chil (cschil) complexed with N,N'- diacetylchitobiose
Analyse Crystal structure of the catalytic domain of chitiniphilus shinanonensis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KXL
- Type
- protein
- Length
- 735 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Family 18 chitinase
- UniProt
- F8WSX2
- Ligands
- NAG
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Family 18 chitinase | protein | 368 | 33% helix, 23% strand | F8WSX2 |
| B | Family 18 chitinase | protein | 367 | 34% helix, 22% strand | F8WSX2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- MLI · Malonate ion · additive · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 3 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
- MXE · 2-methoxyethanol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 628 | 0.71 | 0.78 | 58 | NAG, MLI, PG4 |
| 2 | 614 | 0.70 | 0.78 | 59 | NAG, MXE, PG4 |
| 3 | 286 | 0.55 | 0.76 | 34 | PGE, PG4 |
Interfaces
1 interface between chains.
- A–B · 818 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6KXL · Crystal structure of the catalytic domain of Chitiniphilus shina nsis chitinase ChiL… · 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 F8WSX2
- Elsewhere: RCSB PDB 6KXL · PDBe 6KXL · UniProt F8WSX2
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