MolNFT v1 · #128104 · protein
Lybatide 2, a cystine-rich peptide from lycium barbarum
5NGN: “Lybatide 2, a cystine-rich peptide from lycium barbarum”. X-ray diffraction, 1 ligand (CCN). MolNFT v1 #128104 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5NGN
- Type
- protein
- Length
- 98 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lybatide 2
- Ligands
- CCN
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lybatide 2 | protein | 32 | 47% helix, 0% strand | — |
| B, C | Lybatide 2 | protein | 33 | 45% helix, 0% strand | — |
Ligands and binding sites
- CCN · Acetonitrile · ligand · 4 copies · chains A, C
- GOL · Glycerol · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
2 interfaces between chains.
- A–C · 425 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 316 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 5NGN · Lybatide 2, a cystine-rich peptide from Lycium barbarum · 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
- Elsewhere: RCSB PDB 5NGN · PDBe 5NGN
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