Research workbench
Crystal structure the escherichia COLI CAS1-CAS2 complex bound to protospacer DNA and mg
Analyse Crystal structure the escherichia COLI CAS1-CAS2 complex bound to protospacer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DS5
- Type
- protein + DNA
- Length
- 1,298 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR-associated endonuclease CAS1; CRISPR-associated endoribonuclease CAS2; DNA (28-mer)
- EC
- 3.1.-.-
- UniProt
- Q46896, P45956
- Ligands
- MG
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 7 distinct chains · 52% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated endonuclease CAS1 (EC 3.1.-.-) | protein | 250 | 56% helix, 13% strand | Q46896 |
| B | CRISPR-associated endonuclease CAS1 (EC 3.1.-.-) | protein | 277 | 54% helix, 15% strand | Q46896 |
| C | CRISPR-associated endonuclease CAS1 (EC 3.1.-.-) | protein | 252 | 56% helix, 13% strand | Q46896 |
| D | CRISPR-associated endonuclease CAS1 (EC 3.1.-.-) | protein | 275 | 53% helix, 14% strand | Q46896 |
| E, F | CRISPR-associated endoribonuclease CAS2 (EC 3.1.-.-) | protein | 94 | 22% helix, 46% strand | P45956 |
| G | DNA (28-mer) | dna | 28 | — | — |
| H | DNA (28-mer) | dna | 28 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 5 copies · chains B, E, F, D, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1110 | 0.81 | 0.82 | 82 | empty |
| 2 | 1091 | 0.79 | 0.81 | 80 | empty |
| 3 | 627 | 0.77 | 0.83 | 44 | empty |
| 4 | 733 | 0.73 | 0.79 | 47 | MG |
| 5 | 733 | 0.72 | 0.78 | 41 | MG |
Interfaces
20 interfaces between chains.
- A–B · 1730 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1677 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1255 Ų buried · 4 hydrogen bonds · protein-protein
- G–H · 1004 Ų buried · 111 hydrogen bonds · nucleic-nucleic
- B–F · 793 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5DS5 · Crystal structure the Escherichia coli Cas1-Cas2 complex bound to protospacer DNA and Mg · the same entry in another collection · chain H against H, TM-score 1.00
- Q46896 · AlphaFold monomer V2.0 prediction for CRISPR-associated endonuclease CAS1 (Q46896) · a predicted model of the same protein · chain D against A, TM-score 0.96
- P45956 · AlphaFold monomer V2.0 prediction for CRISPR-associated endoribonuclease CAS2 (P45956) · a predicted model of the same protein · chain F against A, TM-score 0.96
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
- Every structure of UniProt P45956
- Elsewhere: RCSB PDB 5DS5 · PDBe 5DS5 · UniProt Q46896 · UniProt P45956
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