MolNFT v1 · #72842 · protein
High resolution structure of the C-terminal domain crisp-associated protein CAS1 from escherichia COLI str. K-12
3NKE · Protein ygbt: “High resolution structure of the C-terminal domain crisp-associated protein CAS1 from escherichia COLI str.…”. X-ray diffraction, 2 ligands (SO4, SO3), 12 pockets (best druggability 0.71). MolNFT v1 #72842 on…
- PDB
- 3NKE
- Type
- protein
- Length
- 548 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein ygbt
- UniProt
- Q46896
- Ligands
- SO4, SO3
- Pockets
- 12 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein ygbt | protein | 183 | 69% helix, 0% strand | Q46896 |
| B | Protein ygbt | protein | 183 | 69% helix, 0% strand | Q46896 |
| C | Protein ygbt | protein | 182 | 70% helix, 0% strand | Q46896 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, C, B
- SO3 · Sulfite ion · ion · 2 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 111 | 0.71 | 0.92 | 24 | empty |
| 2 | 65 | 0.71 | 0.96 | 18 | empty |
| 3 | 314 | 0.69 | 0.83 | 49 | empty |
| 4 | 273 | 0.65 | 0.82 | 45 | EDO |
| 5 | 205 | 0.45 | 0.74 | 32 | SO4 |
Interfaces
3 interfaces between chains.
- A–C · 898 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 825 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 735 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (engineered).
Compared structures
- 3NKE · High resolution structure of the C-terminal domain CRISP-associated protein Cas1 from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q46896 · AlphaFold monomer V2.0 prediction for CRISPR-associated endonuclease CAS1 (Q46896) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q46896
- Elsewhere: RCSB PDB 3NKE · PDBe 3NKE · UniProt Q46896
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