MolNFT v1 · #34351 · protein
Crystal structure of pseudecin from pseudechis porphyriacus
2DDB: “Crystal structure of pseudecin from pseudechis porphyriacus”. X-ray diffraction, 1 ligand (NA), 11 pockets (best druggability 0.78). MolNFT v1 #34351 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2DDB
- Type
- protein
- Length
- 832 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pseudecin
- UniProt
- Q8AVA3
- Ligands
- NA
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Pseudecin | protein | 207 | 32% helix, 22% strand | Q8AVA3 |
| B, D | Pseudecin | protein | 209 | 32% helix, 22% strand | Q8AVA3 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- FMT · Formic acid · additive · 21 copies · chains A, B, C, D
- GOL · Glycerol · additive · 6 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 906 | 0.78 | 0.80 | 74 | FMT |
| 2 | 416 | 0.67 | 0.80 | 45 | FMT |
| 3 | 294 | 0.60 | 0.78 | 41 | GOL |
| 4 | 116 | 0.50 | 0.81 | 28 | empty |
| 5 | 227 | 0.49 | 0.75 | 27 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1348 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 583 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 581 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 79 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 61 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide (disulfide).
Compared structures
- 2DDB · Crystal structure of pseudecin from Pseudechis porphyriacus · the same entry in another collection · chain D against D, TM-score 1.00
- Q8AVA3 · AlphaFold monomer V2.0 prediction for cysteine-rich venom protein pseudecin (Q8AVA3) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q8AVA3
- Elsewhere: RCSB PDB 2DDB · PDBe 2DDB · UniProt Q8AVA3
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