MolNFT v1 · #122032 · protein
Crystal structure of CGL1 from crassostrea gigas, ligand free form (CGL1/FREE)
5ID8 · Natterin-3: “Crystal structure of CGL1 from crassostrea gigas, ligand free form (CGL1/FREE)”. X-ray diffraction, 5 pockets (best druggability 0.69). MolNFT v1 #122032 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ID8
- Type
- protein
- Length
- 568 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Natterin-3
- UniProt
- K1QRB6
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 62% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Natterin-3 | protein | 142 | 0% helix, 62% strand | K1QRB6 |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 752 | 0.69 | 0.76 | 61 | empty |
| 2 | 231 | 0.59 | 0.80 | 29 | empty |
| 3 | 291 | 0.54 | 0.76 | 26 | empty |
| 4 | 67 | 0.37 | 0.78 | 15 | empty |
| 5 | 70 | 0.29 | 0.73 | 19 | empty |
Interfaces
5 interfaces between chains.
- B–D · 295 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 284 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 183 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 104 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 36 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 5ID8 · Crystal structure of CGL1 from Crassostrea gigas, ligand free form (CGL1/FREE) · 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 K1QRB6
- Elsewhere: RCSB PDB 5ID8 · PDBe 5ID8 · UniProt K1QRB6
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