Research workbench
Crystal structure of zinc-bound pseudecin from pseudechis porphyriacus
Analyse Crystal structure of zinc-bound pseudecin from pseudechis porphyriacus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EPF
- Type
- protein
- Length
- 828 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pseudecin
- UniProt
- Q8AVA3
- Ligands
- ZN, NA
- Pockets
- 14 · 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 | Pseudecin | protein | 207 | 32% helix, 22% strand | Q8AVA3 |
Ligands and binding sites
- ZN · Zinc ion · metal · 5 copies · chains A, B, C, D
- NA · Sodium ion · metal · 3 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 707 | 0.80 | 0.85 | 71 | empty |
| 2 | 488 | 0.76 | 0.84 | 56 | empty |
| 3 | 434 | 0.75 | 0.84 | 42 | empty |
| 4 | 52 | 0.69 | 0.97 | 19 | empty |
| 5 | 492 | 0.63 | 0.76 | 44 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1225 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 794 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 408 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide (disulfide).
Compared structures
- 2EPF · Crystal Structure of Zinc-Bound 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 D 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 Q8AVA3
- Elsewhere: RCSB PDB 2EPF · PDBe 2EPF · UniProt Q8AVA3
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