Research workbench
Volvatoxin A2 in monoclinic crystal
Analyse Volvatoxin A2 in monoclinic crystal in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PP0
- Type
- protein
- Length
- 770 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Volvatoxin A2
- UniProt
- Q6USC4
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Volvatoxin A2 | protein | 191 | 31% helix, 40% strand | Q6USC4 |
| B, C | Volvatoxin A2 | protein | 194 | 30% helix, 40% strand | Q6USC4 |
Ligands and binding sites
- ACY · Acetic acid · additive · 13 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1052 | 0.75 | 0.78 | 100 | empty |
| 2 | 85 | 0.54 | 0.85 | 15 | ACY |
| 3 | 242 | 0.51 | 0.75 | 23 | empty |
| 4 | 164 | 0.49 | 0.77 | 29 | ACY |
| 5 | 238 | 0.47 | 0.73 | 39 | ACY |
Interfaces
4 interfaces between chains.
- C–D · 647 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 626 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 407 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 374 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1PP0 · volvatoxin A2 in monoclinic crystal · 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 Q6USC4
- Elsewhere: RCSB PDB 1PP0 · PDBe 1PP0 · UniProt Q6USC4
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