MolNFT v1 · #38344 · protein
Crystal structure of a complex of griffithsin with mannose at 0.94 a resolution
2GUD: “Crystal structure of a complex of griffithsin with mannose at 0.94 a resolution”. X-ray diffraction, 4 ligands (ACE, MAN, BMA), 2 pockets (best druggability 0.45). MolNFT v1 #38344 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2GUD
- Type
- protein
- Length
- 242 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Griffithsin
- UniProt
- P84801
- Ligands
- ACE, MAN, BMA, SO4
- Pockets
- 2 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 64% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Griffithsin | protein | 121 | 0% helix, 64% strand | P84801 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.45 | 0.77 | 25 | empty |
| 2 | 63 | 0.43 | 0.82 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2216 Ų buried · 53 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2GUD · Crystal structure of a complex of griffithsin with mannose at 0.94 A resolution · 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 P84801
- Elsewhere: RCSB PDB 2GUD · PDBe 2GUD · UniProt P84801
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