MolNFT v1 · #139874 · protein
Crystal structure of an archaeal chitinase in the substrate-complex form (P63)
5XSW: “Crystal structure of an archaeal chitinase in the substrate-complex form (P63)”. X-ray diffraction, 3 ligands (NDG, NAG, PO4), 6 pockets (best druggability 0.78). MolNFT v1 #139874 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5XSW
- Type
- protein
- Length
- 970 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chitinase
- EC
- 3.2.1.14
- UniProt
- A0A161KIT4
- Ligands
- NDG, NAG, PO4
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Chitinase (EC 3.2.1.14) | protein | 485 | 39% helix, 19% strand | A0A161KIT4 |
Ligands and binding sites
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 12 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 782 | 0.78 | 0.82 | 78 | NDG, NAG, PO4, GOL |
| 2 | 402 | 0.70 | 0.82 | 28 | GOL |
| 3 | 142 | 0.46 | 0.77 | 19 | GOL |
| 4 | 140 | 0.45 | 0.77 | 20 | GOL |
| 5 | 81 | 0.38 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1290 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 5XSW · Crystal structure of an archaeal chitinase in the substrate-complex form (P63) · 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 A0A161KIT4
- Elsewhere: RCSB PDB 5XSW · PDBe 5XSW · UniProt A0A161KIT4
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