MolNFT v1 · #142126 · protein
Crystal structure of lamprey immune protein
5ZU4 · Natterin-like protein: “Crystal structure of lamprey immune protein”. X-ray diffraction, 1 ligand (CL), 6 pockets (best druggability 0.67). MolNFT v1 #142126 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ZU4
- Type
- protein
- Length
- 627 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Natterin-like protein
- UniProt
- K7WEH5
- Ligands
- CL
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 63% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Natterin-like protein | protein | 313 | 2% helix, 63% strand | K7WEH5 |
| B | Natterin-like protein | protein | 314 | 3% helix, 63% strand | K7WEH5 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 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 | 180 | 0.67 | 0.86 | 33 | EDO, PEG |
| 2 | 156 | 0.64 | 0.86 | 34 | EDO |
| 3 | 50 | 0.39 | 0.82 | 15 | EDO |
| 4 | 91 | 0.34 | 0.74 | 16 | CL |
| 5 | 57 | 0.25 | 0.71 | 13 | CL |
Interfaces
1 interface between chains.
- A–B · 1669 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5ZU4 · Crystal structure of Lamprey immune protein · 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 K7WEH5
- Elsewhere: RCSB PDB 5ZU4 · PDBe 5ZU4 · UniProt K7WEH5
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