Research workbench
Crystal structure of natrin from naja atra snake venom
Analyse Crystal structure of natrin from naja atra snake venom in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XX5
- Type
- protein
- Length
- 644 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Natrin 1
- UniProt
- Q7T1K6
- Pockets
- 10 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Natrin 1 | protein | 216 | 31% helix, 19% strand | Q7T1K6 |
| C | Natrin 1 | protein | 212 | 32% helix, 19% strand | Q7T1K6 |
Ligands and binding sites
- EOH · Ethanol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 361 | 0.67 | 0.81 | 53 | empty |
| 2 | 319 | 0.56 | 0.76 | 34 | empty |
| 3 | 187 | 0.56 | 0.80 | 26 | empty |
| 4 | 241 | 0.52 | 0.76 | 47 | empty |
| 5 | 268 | 0.51 | 0.74 | 30 | empty |
Interfaces
3 interfaces between chains.
- A–B · 690 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 541 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 431 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 1XX5 · Crystal Structure of Natrin from Naja atra snake venom · 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 0.98
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 Q7T1K6
- Elsewhere: RCSB PDB 1XX5 · PDBe 1XX5 · UniProt Q7T1K6
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