MolNFT v1 · #122034 · protein
Crystal structure of CGL1 from crassostrea gigas, mannose-bound form (CGL1/MAN)
5IDA · Natterin-3: “Crystal structure of CGL1 from crassostrea gigas, mannose-bound form (CGL1/MAN)”. X-ray diffraction, 1 ligand (BMA), 5 pockets (best druggability 0.69). MolNFT v1 #122034 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5IDA
- Type
- protein
- Length
- 568 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Natterin-3
- UniProt
- K1QRB6
- Ligands
- BMA
- 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 |
Ligands and binding sites
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 759 | 0.69 | 0.76 | 69 | BMA |
| 2 | 228 | 0.58 | 0.79 | 29 | empty |
| 3 | 267 | 0.54 | 0.76 | 26 | empty |
| 4 | 78 | 0.41 | 0.79 | 15 | empty |
| 5 | 80 | 0.30 | 0.72 | 21 | empty |
Interfaces
5 interfaces between chains.
- B–D · 277 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 266 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 219 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 101 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
- 5IDA · Crystal structure of CGL1 from Crassostrea gigas, mannose-bound form (CGL1/MAN) · 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 5IDA · PDBe 5IDA · UniProt K1QRB6
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