Research workbench
Exploring cystine dense peptide space to open a unique molecular toolbox
Analyse Exploring cystine dense peptide space to open a unique molecular toolbox in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AUP
- Type
- protein
- Length
- 608 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Potassium channel toxin gamma-ktx 2.2
- UniProt
- P59938
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, F, D, E, G, H, I, J, K, L, M, N, O, P | Potassium channel toxin gamma-ktx 2.2 | protein | 38 | 32% helix, 37% strand | P59938 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 21 copies · chains A, B, C, F, G, E, D, P, H, J, L, I, K, M, N, O
- GOL · Glycerol · additive · 6 copies · chains A, B, D, E, P, G, K, I, L, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 364 | 0.80 | 0.90 | 58 | empty |
| 2 | 93 | 0.73 | 0.96 | 27 | SO4 |
| 3 | 55 | 0.70 | 0.97 | 13 | SO4 |
| 4 | 430 | 0.66 | 0.79 | 52 | SO4, GOL |
| 5 | 68 | 0.66 | 0.93 | 12 | SO4 |
Interfaces
40 interfaces between chains.
- D–E · 455 Ų buried · 7 hydrogen bonds · protein-protein
- M–N · 430 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 429 Ų buried · 5 hydrogen bonds · protein-protein
- C–F · 428 Ų buried · 3 hydrogen bonds · protein-protein
- I–J · 426 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide (disulfide).
Compared structures
- 6AUP · Exploring Cystine Dense Peptide Space to Open a Unique Molecular Toolbox · the same entry in another collection · chain P against P, 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 P59938
- Elsewhere: RCSB PDB 6AUP · PDBe 6AUP · UniProt P59938
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