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Crystal structure of ntri homodimer
Analyse Crystal structure of ntri homodimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DLF
- Type
- protein
- Length
- 470 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neurotrimin
- UniProt
- Q9P121
- Ligands
- NAG
- Pockets
- 3 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neurotrimin | protein | 236 | 3% helix, 57% strand | Q9P121 |
| B | Neurotrimin | protein | 234 | 3% helix, 58% strand | Q9P121 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains B, 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 90 | 0.50 | 0.82 | 21 | NAG |
| 2 | 133 | 0.45 | 0.77 | 22 | NAG |
| 3 | 63 | 0.32 | 0.76 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 793 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
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 Q9P121
- Elsewhere: RCSB PDB 6DLF · PDBe 6DLF · UniProt Q9P121
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