MolNFT v1 · #170993 · protein
Crystal structure of the human neuronal pentraxin 1 (NP1) pentraxin (ptx) domain.
6YPE · Neuronal pentraxin-1: “Crystal structure of the human neuronal pentraxin 1 (NP1) pentraxin (ptx) domain.”. X-ray diffraction, 1 ligand (CA), 4 pockets (best druggability 0.66). MolNFT v1 #170993 on GenesisL1: 3D structure, binding…
- PDB
- 6YPE
- Type
- protein
- Length
- 410 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuronal pentraxin-1
- UniProt
- Q15818
- Ligands
- CA
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Neuronal pentraxin-1 | protein | 205 | 8% helix, 44% strand | Q15818 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B
- CAC · Cacodylate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 245 | 0.66 | 0.83 | 39 | CAC |
| 2 | 102 | 0.44 | 0.79 | 18 | empty |
| 3 | 89 | 0.41 | 0.78 | 19 | empty |
| 4 | 91 | 0.34 | 0.74 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 352 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6YPE · Crystal structure of the human neuronal pentraxin 1 (NP1) pentraxin (PTX) domain. · the same entry in another collection · chain A against A, TM-score 1.00
- Q15818 · AlphaFold monomer V2.0 prediction for neuronal pentraxin-1 (Q15818) · a predicted model of the same protein · 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 Q15818
- Elsewhere: RCSB PDB 6YPE · PDBe 6YPE · UniProt Q15818
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.