Research workbench
Crystal structure of a five site mutated cyanovirin-N with a mannose dimer bound at 1.8 a resolution
Analyse Crystal structure of a five site mutated cyanovirin-N with a mannose dimer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PYS
- Type
- protein
- Length
- 204 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyanovirin-N
- UniProt
- P81180
- Ligands
- MAN
- Pockets
- 2 · best druggability 0.39
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyanovirin-N | protein | 101 | 14% helix, 57% strand | P81180 |
| B | Cyanovirin-N | protein | 103 | 13% helix, 56% strand | P81180 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
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 | 79 | 0.39 | 0.78 | 14 | empty |
| 2 | 122 | 0.37 | 0.73 | 20 | MAN |
Interfaces
1 interface between chains.
- A–B · 558 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2PYS · Crystal Structure of a Five Site Mutated Cyanovirin-N with a Mannose Dimer Bound at 1.8 A… · the same entry in another collection · chain A against A, TM-score 1.00
- P81180 · AlphaFold monomer V2.0 prediction for cyanovirin-N (P81180) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P81180
- Elsewhere: RCSB PDB 2PYS · PDBe 2PYS · UniProt P81180
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