Research workbench
E. far CAS1-CAS2/PRESPACER binary complex
Analyse E. far CAS1-CAS2/PRESPACER binary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XVN
- Type
- protein + DNA
- Length
- 2,786 residues
- Chains
- 16
- 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
- E6GPD7, E6GPD6
- Ligands
- MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 8 distinct chains · 47% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, I, K | CRISPR-associated endonuclease CAS1 (EC 3.1.-.-) | protein | 285 | 49% helix, 19% strand | E6GPD7 |
| B, J, L | CRISPR-associated endonuclease CAS1 (EC 3.1.-.-) | protein | 288 | 50% helix, 18% strand | E6GPD7 |
| D | CRISPR-associated endonuclease CAS1 (EC 3.1.-.-) | protein | 259 | 49% helix, 20% strand | E6GPD7 |
| E, N | CRISPR-associated endoribonuclease CAS2 (EC 3.1.-.-) | protein | 104 | 36% helix, 33% strand | E6GPD6 |
| F, M | CRISPR-associated endoribonuclease CAS2 (EC 3.1.-.-) | protein | 108 | 34% helix, 29% strand | E6GPD6 |
| G | DNA (28-mer) | dna | 25 | — | — |
| H, P | DNA (28-mer) | dna | 24 | — | — |
| O | DNA (28-mer) | dna | 26 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains E, F, H, G, M, N, P, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 169 | 0.82 | 0.97 | 29 | empty |
| 2 | 132 | 0.80 | 0.97 | 28 | empty |
| 3 | 120 | 0.80 | 0.98 | 24 | empty |
| 4 | 125 | 0.79 | 0.97 | 23 | empty |
| 5 | 653 | 0.71 | 0.79 | 63 | empty |
Interfaces
35 interfaces between chains.
- K–L · 2023 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2010 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1979 Ų buried · 33 hydrogen bonds · protein-protein
- I–J · 1950 Ų buried · 33 hydrogen bonds · protein-protein
- E–F · 1569 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 5XVN · E. far Cas1-Cas2/prespacer binary complex · the same entry in another collection · chain A against A, 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 E6GPD7
- Every structure of UniProt E6GPD6
- Elsewhere: RCSB PDB 5XVN · PDBe 5XVN · UniProt E6GPD7 · UniProt E6GPD6
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