MolNFT v1 · #158789 · protein
Racemic melittin
6O4M · D-melittin: “Racemic melittin”. X-ray diffraction, 2 ligands (SO4, NH2), 1 pocket (best druggability 0.46). MolNFT v1 #158789 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6O4M
- Type
- protein
- Length
- 104 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-melittin
- UniProt
- P01501
- Ligands
- SO4, NH2
- Pockets
- 1 · best druggability 0.46
Structure
x-ray diffraction · 1 distinct chain · 88% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A, B, C | D-melittin | protein | 26 | 88% helix, 0% strand | P01501 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 9 copies · chains D, A, B, C
- NH2 · Amino group · ion · 4 copies · chains D, A, B, C
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 | 191 | 0.46 | 0.75 | 28 | empty |
Interfaces
4 interfaces between chains.
- A–B · 469 Ų buried · 1 hydrogen bond · protein-protein
- D–A · 448 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 243 Ų buried · 0 hydrogen bonds · protein-protein
- D–B · 68 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 46 d-amino (D-amino acid).
Compared structures
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 P01501
- Elsewhere: RCSB PDB 6O4M · PDBe 6O4M · UniProt P01501
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