Research workbench
Structural basis for DNase activity of a conserved protein implicated in CRISPR-mediated antiviral defense
Analyse Structural basis for DNase activity of a conserved protein implicated in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GOD
- Type
- protein
- Length
- 1,231 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CAS1
- UniProt
- Q02ML7
- Ligands
- MN, NA, CA
- Pockets
- 15 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 55% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CAS1 | protein | 320 | 54% helix, 16% strand | Q02ML7 |
| B | CAS1 | protein | 319 | 55% helix, 16% strand | Q02ML7 |
| C | CAS1 | protein | 293 | 56% helix, 12% strand | Q02ML7 |
| D | CAS1 | protein | 299 | 55% helix, 12% strand | Q02ML7 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 188 | 0.83 | 0.97 | 32 | empty |
| 2 | 172 | 0.82 | 0.97 | 29 | empty |
| 3 | 474 | 0.71 | 0.81 | 58 | empty |
| 4 | 368 | 0.69 | 0.82 | 56 | empty |
| 5 | 745 | 0.69 | 0.76 | 67 | MN |
Interfaces
5 interfaces between chains.
- A–C · 1837 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 1822 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 389 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 381 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 346 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3GOD · Structural basis for DNase activity of a conserved protein implicated in CRISPR-mediated… · the same entry in another collection · chain D against D, TM-score 1.00
- Q02ML7 · AlphaFold monomer V2.0 prediction for CRISPR-associated endonuclease CAS1 (Q02ML7) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q02ML7
- Elsewhere: RCSB PDB 3GOD · PDBe 3GOD · UniProt Q02ML7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.