Research workbench
Crystal structure of human cartilage GP39 (hc-GP39) in complex with chitopentaose
Analyse Crystal structure of human cartilage GP39 (hc-GP39) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NWT
- 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
- 13 · 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 · 26 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
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 591 | 0.71 | 0.80 | 35 | empty |
| 2 | 452 | 0.67 | 0.79 | 53 | NAG, NDG |
| 3 | 421 | 0.66 | 0.79 | 55 | NAG, NDG |
| 4 | 477 | 0.66 | 0.78 | 57 | NDG, NAG |
| 5 | 450 | 0.66 | 0.78 | 53 | NAG, NDG |
Interfaces
1 interface between chains.
- C–D · 438 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 1NWT · Crystal structure of human cartilage gp39 (HC-gp39) in complex with chitopentaose · 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 1NWT · PDBe 1NWT · UniProt P36222
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