MolNFT v1 · #169268 · protein
Peptide-bound structure of marinomonas primoryensis peptide-binding domain
6X6M · Antifreeze protein: “Peptide-bound structure of marinomonas primoryensis peptide-binding domain”. X-ray diffraction, 1 ligand (CA), 1 pocket (best druggability 0.45). MolNFT v1 #169268 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6X6M
- Type
- protein
- Length
- 510 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antifreeze protein; Peptide
- UniProt
- A1YIY3
- Ligands
- CA
- Pockets
- 1 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antifreeze protein | protein | 506 | 5% helix, 53% strand | A1YIY3 |
| B | Peptide | protein | 4 | 0% helix, 25% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.45 | 0.73 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 297 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6X6M · Peptide-bound structure of Marinomonas primoryensis peptide-binding domain · 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 A1YIY3
- Elsewhere: RCSB PDB 6X6M · PDBe 6X6M · UniProt A1YIY3
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