Research workbench
Crystal structure of zinc-bound natrin from naja atra
Analyse Crystal structure of zinc-bound natrin from naja atra in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MZ8
- Type
- protein
- Length
- 440 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Natrin-1
- UniProt
- Q7T1K6
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Natrin-1 | protein | 220 | 34% helix, 19% strand | Q7T1K6 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1091 | 0.71 | 0.75 | 78 | empty |
| 2 | 275 | 0.51 | 0.74 | 38 | empty |
| 3 | 219 | 0.48 | 0.74 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 296 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 3MZ8 · Crystal Structure of Zinc-Bound Natrin From Naja atra · the same entry in another collection · chain A against A, TM-score 1.00
- Q7T1K6 · AlphaFold monomer V2.0 prediction for cysteine-rich venom protein natrin-1 (Q7T1K6) · a predicted model of the same protein · chain A 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 Q7T1K6
- Elsewhere: RCSB PDB 3MZ8 · PDBe 3MZ8 · UniProt Q7T1K6
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