MolNFT v1 · #137666 · protein + DNA
CAS1-CAS2 bound to full-site mimic
5VVK · CRISPR-associated endonuclease CAS1: “CAS1-CAS2 bound to full-site mimic”. X-ray diffraction, 20 pockets (best druggability 0.81). MolNFT v1 #137666 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5VVK
- Type
- protein + DNA
- Length
- 1,364 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
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 9 distinct chains · 52% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated endonuclease CAS1 (EC 3.1.-.-) | protein | 266 | 53% helix, 15% strand | Q46896 |
| B | CRISPR-associated endonuclease CAS1 (EC 3.1.-.-) | protein | 263 | 56% helix, 15% strand | Q46896 |
| C | CRISPR-associated endonuclease CAS1 (EC 3.1.-.-) | protein | 267 | 54% helix, 14% strand | Q46896 |
| D | CRISPR-associated endonuclease CAS1 (EC 3.1.-.-) | protein | 272 | 54% helix, 15% strand | Q46896 |
| E, F | CRISPR-associated endoribonuclease CAS2 (EC 3.1.-.-) | protein | 94 | 26% helix, 46% strand | P45956 |
| G | DNA (5'-D(*GP*CP*CP*CP*CP*AP*GP*TP*AP*GP*C)-3') | dna | 11 | — | — |
| H | DNA (5'-D(*GP*AP*CP*CP*AP*CP*CP*AP*GP*TP*G)-3') | dna | 11 | — | — |
| J | DNA (58-mer) | dna | 43 | — | — |
| K | DNA (58-mer) | dna | 43 | — | — |
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1118 | 0.81 | 0.82 | 90 | empty |
| 2 | 1176 | 0.80 | 0.82 | 79 | empty |
| 3 | 494 | 0.73 | 0.82 | 35 | empty |
| 4 | 750 | 0.73 | 0.79 | 49 | empty |
| 5 | 714 | 0.71 | 0.78 | 42 | empty |
Interfaces
29 interfaces between chains.
- A–B · 1757 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1680 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1217 Ų buried · 8 hydrogen bonds · protein-protein
- C–K · 1110 Ų buried · 26 hydrogen bonds · protein-nucleic
- A–J · 1076 Ų buried · 23 hydrogen bonds · protein-nucleic
Compared structures
- 5VVK · Cas1-Cas2 bound to full-site mimic · 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 B 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 5VVK · PDBe 5VVK · UniProt Q46896 · UniProt P45956
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