MolNFT v1 · #28172 · protein
A 2.4 crystal structure of conkunitzin-S1, a novel kunitz- fold cone snail neurotoxin.
1Y62: “A 2.4 crystal structure of conkunitzin-S1, a novel kunitz- fold cone snail neurotoxin.”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.34). MolNFT v1 #28172 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1Y62
- Type
- protein
- Length
- 336 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Conkunitzin-S1
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.34
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Conkunitzin-S1 | protein | 56 | 21% helix, 27% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 15 copies · chains A, B, D, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.34 | 0.75 | 16 | SO4 |
| 2 | 67 | 0.33 | 0.76 | 15 | SO4 |
| 3 | 61 | 0.28 | 0.74 | 22 | empty |
Interfaces
5 interfaces between chains.
- A–F · 463 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 404 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 336 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 192 Ų buried · 0 hydrogen bonds · protein-protein
- A–E · 23 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 1Y62 · A 2.4 crystal structure of conkunitzin-S1, a novel Kunitz-fold cone snail neurotoxin. · the same entry in another collection · chain B against B, 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 1Y62 · PDBe 1Y62
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