MolNFT v1 · #137665 · protein + DNA
CAS1-CAS2 bound to half-site intermediate
5VVJ · CRISPR-associated endonuclease CAS1: “CAS1-CAS2 bound to half-site intermediate”. X-ray diffraction, 18 pockets (best druggability 0.81). MolNFT v1 #137665 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5VVJ
- Type
- protein + DNA
- Length
- 1,352 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…
- EC
- 3.1.-.-
- UniProt
- Q46896, P45956
- Pockets
- 18 · best druggability 0.81
Structure
x-ray diffraction · 8 distinct chains · 49% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated endonuclease CAS1 (EC 3.1.-.-) | protein | 262 | 52% helix, 12% strand | Q46896 |
| B | CRISPR-associated endonuclease CAS1 (EC 3.1.-.-) | protein | 269 | 52% helix, 16% strand | Q46896 |
| C | CRISPR-associated endonuclease CAS1 (EC 3.1.-.-) | protein | 253 | 55% helix, 13% strand | Q46896 |
| D | CRISPR-associated endonuclease CAS1 (EC 3.1.-.-) | protein | 265 | 53% helix, 15% strand | Q46896 |
| E | CRISPR-associated endoribonuclease CAS2 (EC 3.1.-.-) | protein | 93 | 26% helix, 44% strand | P45956 |
| F | CRISPR-associated endoribonuclease CAS2 (EC 3.1.-.-) | protein | 95 | 25% helix, 45% strand | P45956 |
| G | DNA (28-mer) | dna | 28 | — | — |
| H | DNA (112-mer) | dna | 87 | — | — |
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1176 | 0.81 | 0.83 | 93 | empty |
| 2 | 1008 | 0.81 | 0.82 | 76 | empty |
| 3 | 698 | 0.77 | 0.82 | 46 | empty |
| 4 | 623 | 0.74 | 0.81 | 64 | empty |
| 5 | 738 | 0.72 | 0.79 | 43 | empty |
Interfaces
20 interfaces between chains.
- A–B · 1761 Ų buried · 16 hydrogen bonds · protein-protein
- A–H · 1754 Ų buried · 33 hydrogen bonds · protein-nucleic
- C–D · 1696 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1253 Ų buried · 6 hydrogen bonds · protein-protein
- G–H · 1039 Ų buried · 73 hydrogen bonds · nucleic-nucleic
Compared structures
- 5VVJ · Cas1-Cas2 bound to half-site intermediate · 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 B against A, TM-score 0.97
- 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 0.96
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 5VVJ · PDBe 5VVJ · UniProt Q46896 · UniProt P45956
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