MolNFT v1 · #155637 · protein
Crystal structure of CECHT1, a nematode I family chitinase from C. elegans
6LDU · Probable endochitinase: “Crystal structure of CECHT1, a nematode I family chitinase from C. elegans”. X-ray diffraction, 1 ligand (NAG), 3 pockets (best druggability 0.63). MolNFT v1 #155637 on GenesisL1: 3D structure, binding sites…
- PDB
- 6LDU
- Type
- protein
- Length
- 383 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable endochitinase
- EC
- 3.2.1.14
- UniProt
- Q11174
- Ligands
- NAG
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable endochitinase (EC 3.2.1.14) | protein | 383 | 36% helix, 22% strand | Q11174 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 353 | 0.63 | 0.79 | 41 | GOL |
| 2 | 84 | 0.39 | 0.77 | 21 | empty |
| 3 | 56 | 0.26 | 0.72 | 13 | empty |
Modifications
Observed in the structure: 2 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6LDU · Crystal structure of CeCht1, a nematode I family chitinase from C. elegans · the same entry in another collection · chain A against A, TM-score 1.00
- Q11174 · AlphaFold monomer V2.0 prediction for probable endochitinase (Q11174) · 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 Q11174
- Elsewhere: RCSB PDB 6LDU · PDBe 6LDU · UniProt Q11174
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