Research workbench
CAS1-CAS2 bound to full-site mimic with ni
Analyse CAS1-CAS2 bound to full-site mimic with ni in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VVL
- Type
- protein + DNA
- Length
- 1,361 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR-associated endonuclease CAS1; CRISPR-associated endoribonuclease CAS2; DNA…
- EC
- 3.1.-.-
- UniProt
- Q46896, P45956
- Ligands
- NI
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 10 distinct chains · 49% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated endonuclease CAS1 (EC 3.1.-.-) | protein | 264 | 53% helix, 14% strand | Q46896 |
| B | CRISPR-associated endonuclease CAS1 (EC 3.1.-.-) | protein | 273 | 53% helix, 15% strand | Q46896 |
| C | CRISPR-associated endonuclease CAS1 (EC 3.1.-.-) | protein | 267 | 53% helix, 13% strand | Q46896 |
| D | CRISPR-associated endonuclease CAS1 (EC 3.1.-.-) | protein | 271 | 52% helix, 15% strand | Q46896 |
| E | CRISPR-associated endoribonuclease CAS2 (EC 3.1.-.-) | protein | 94 | 26% helix, 46% strand | P45956 |
| F | CRISPR-associated endoribonuclease CAS2 (EC 3.1.-.-) | protein | 95 | 25% helix, 45% strand | P45956 |
| G | DNA (11-mer) | dna | 11 | — | — |
| H | DNA (11-mer) | dna | 11 | — | — |
| J | DNA (58-mer) | dna | 41 | — | — |
| K | DNA (58-mer) | dna | 34 | — | — |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 22 copies · chains A, J, K, H, B, C, D, 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 | 950 | 0.82 | 0.84 | 61 | empty |
| 2 | 708 | 0.77 | 0.82 | 84 | empty |
| 3 | 405 | 0.75 | 0.85 | 32 | empty |
| 4 | 722 | 0.73 | 0.79 | 48 | NI |
| 5 | 271 | 0.72 | 0.86 | 43 | empty |
Interfaces
29 interfaces between chains.
- A–B · 1673 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1671 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1249 Ų buried · 7 hydrogen bonds · protein-protein
- C–K · 1107 Ų buried · 26 hydrogen bonds · protein-nucleic
- A–J · 1054 Ų buried · 26 hydrogen bonds · protein-nucleic
Compared structures
- 5VVL · Cas1-Cas2 bound to full-site mimic with Ni · the same entry in another collection · chain K against K, TM-score 1.00
- P45956 · AlphaFold monomer V2.0 prediction for CRISPR-associated endoribonuclease CAS2 (P45956) · a predicted model of the same protein · chain E against A, TM-score 0.97
- 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 0.97
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
- Every structure of UniProt P45956
- Elsewhere: RCSB PDB 5VVL · PDBe 5VVL · UniProt Q46896 · UniProt P45956
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