MolNFT v1 · #116698 · protein + DNA
Crystal structure of CAS-DNA-N1 complex
5DLJ · CRISPR-associated endonuclease CAS1: “Crystal structure of CAS-DNA-N1 complex”. X-ray diffraction, 16 pockets (best druggability 0.83). MolNFT v1 #116698 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DLJ
- Type
- protein + DNA
- Length
- 1,328 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR-associated endonuclease CAS1; 39-mer DNA N1-F; 39-mer DNA N1-R; CRISPR-associated…
- EC
- 3.1.-.-
- UniProt
- Q46896, P45956
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A | CRISPR-associated endonuclease CAS1 (EC 3.1.-.-) | protein | 267 | 52% helix, 16% strand | Q46896 |
| C, B | CRISPR-associated endonuclease CAS1 (EC 3.1.-.-) | protein | 280 | 53% helix, 15% strand | Q46896 |
| G | 39-mer DNA N1-F | dna | 39 | — | — |
| H | 39-mer DNA N1-R | dna | 39 | — | — |
| F, E | CRISPR-associated endoribonuclease CAS2 (EC 3.1.-.-) | protein | 78 | 28% helix, 40% strand | P45956 |
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1050 | 0.83 | 0.85 | 107 | empty |
| 2 | 960 | 0.81 | 0.83 | 54 | empty |
| 3 | 1002 | 0.75 | 0.78 | 83 | empty |
| 4 | 382 | 0.70 | 0.83 | 33 | empty |
| 5 | 668 | 0.70 | 0.78 | 45 | empty |
Interfaces
20 interfaces between chains.
- D–C · 1683 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1674 Ų buried · 24 hydrogen bonds · protein-protein
- A–H · 1414 Ų buried · 30 hydrogen bonds · protein-nucleic
- D–G · 1412 Ų buried · 29 hydrogen bonds · protein-nucleic
- F–E · 1137 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5DLJ · Crystal Structure of Cas-DNA-N1 complex · the same entry in another collection · chain E against E, 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 0.99
- Q46896 · AlphaFold monomer V2.0 prediction for CRISPR-associated endonuclease CAS1 (Q46896) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 5DLJ · PDBe 5DLJ · UniProt Q46896 · UniProt P45956
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