Research workbench
CAS1-CAS2-CSN2-DNA complex from the type II-a CRISPR-CAS system
Analyse CAS1-CAS2-CSN2-DNA complex from the type II-a CRISPR-CAS system in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QXF
- Type
- protein + DNA
- Length
- 4,138 residues
- Chains
- 22
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR-associated protein CSN2; CRISPR-associated endonuclease CAS1; CRISPR-associated…
- EC
- 3.1.-.-
- UniProt
- G3ECR4, G3ECR2, G3ECR3
- Ligands
- CA
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 6 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | CRISPR-associated protein CSN2 | protein | 218 | 41% helix, 18% strand | G3ECR4 |
| B, D, F, H | CRISPR-associated protein CSN2 | protein | 219 | 41% helix, 18% strand | G3ECR4 |
| I, J, L, M, O, P, R, S | CRISPR-associated endonuclease CAS1 (EC 3.1.-.-) | protein | 287 | 49% helix, 16% strand | G3ECR2 |
| K, N, Q, T | CRISPR-associated endoribonuclease CAS2 (EC 3.1.-.-) | protein | 11 | 0% helix, 36% strand | G3ECR3 |
| X | DNA (25-mer) | dna | 25 | — | — |
| Y | DNA (25-mer) | dna | 25 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, D, B, C, E, H, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.81 | 0.95 | 45 | empty |
| 2 | 180 | 0.78 | 0.94 | 42 | empty |
| 3 | 976 | 0.77 | 0.79 | 61 | empty |
| 4 | 742 | 0.77 | 0.81 | 52 | empty |
| 5 | 224 | 0.76 | 0.90 | 50 | empty |
Interfaces
45 interfaces between chains.
- B–C · 2180 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 2179 Ų buried · 25 hydrogen bonds · protein-protein
- E–H · 2177 Ų buried · 26 hydrogen bonds · protein-protein
- F–G · 2172 Ų buried · 27 hydrogen bonds · protein-protein
- L–M · 1928 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 6QXF · Cas1-Cas2-Csn2-DNA complex from the Type II-A CRISPR-Cas system · the same entry in another collection · chain K against K, TM-score 1.00
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 G3ECR4
- Every structure of UniProt G3ECR2
- Every structure of UniProt G3ECR3
- Elsewhere: RCSB PDB 6QXF · PDBe 6QXF · UniProt G3ECR4 · UniProt G3ECR2 · UniProt G3ECR3
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