MolNFT v1 · #16369 · protein
Crystal structure of human cartilage GP39 (hc-GP39) in complex with chitotetraose
1NWU · Chitinase-3 like protein 1: “Crystal structure of human cartilage GP39 (hc-GP39) in complex with chitotetraose”. X-ray diffraction, 2 ligands (NAG, NDG), 12 pockets (best druggability 0.71). MolNFT v1 #16369 on GenesisL1: 3D…
- PDB
- 1NWU
- Type
- protein
- Length
- 1,448 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chitinase-3 like protein 1
- UniProt
- P36222
- Ligands
- NAG, NDG
- Pockets
- 12 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Chitinase-3 like protein 1 | protein | 362 | 37% helix, 24% strand | P36222 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 19 copies · chains A, B, C, D
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 579 | 0.71 | 0.80 | 39 | empty |
| 2 | 469 | 0.68 | 0.79 | 50 | NAG, NDG |
| 3 | 423 | 0.66 | 0.79 | 57 | NAG, NDG |
| 4 | 451 | 0.66 | 0.78 | 54 | NDG, NAG |
| 5 | 460 | 0.66 | 0.78 | 53 | NAG, NDG |
Interfaces
1 interface between chains.
- C–D · 429 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 1NWU · Crystal structure of human cartilage gp39 (HC-gp39) in complex with chitotetraose · the same entry in another collection · chain D against D, TM-score 1.00
- P36222 · AlphaFold monomer V2.0 prediction for chitinase-3-like protein 1 (P36222) · a predicted model of the same protein · chain D 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 P36222
- Elsewhere: RCSB PDB 1NWU · PDBe 1NWU · UniProt P36222
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