MolNFT v1 · #34350 · protein
Crystal structure of pseudechetoxin from pseudechis australis
2DDA: “Crystal structure of pseudechetoxin from pseudechis australis”. X-ray diffraction, 1 ligand (NA), 10 pockets (best druggability 0.80). MolNFT v1 #34350 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2DDA
- Type
- protein
- Length
- 832 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pseudechetoxin
- UniProt
- Q8AVA4
- Ligands
- NA
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pseudechetoxin | protein | 208 | 32% helix, 22% strand | Q8AVA4 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- FMT · Formic acid · additive · 6 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1032 | 0.80 | 0.81 | 82 | FMT |
| 2 | 390 | 0.64 | 0.78 | 40 | empty |
| 3 | 93 | 0.59 | 0.87 | 20 | NA |
| 4 | 328 | 0.57 | 0.76 | 37 | empty |
| 5 | 128 | 0.50 | 0.80 | 29 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1520 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 603 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 590 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 77 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 44 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide (disulfide).
Compared structures
- 2DDA · Crystal structure of pseudechetoxin from Pseudechis australis · the same entry in another collection · chain D against D, TM-score 1.00
- Q8AVA4 · AlphaFold monomer V2.0 prediction for cysteine-rich venom protein pseudechetoxin (Q8AVA4) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q8AVA4
- Elsewhere: RCSB PDB 2DDA · PDBe 2DDA · UniProt Q8AVA4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.