Research workbench
Crystal structure of CAS-DNA-pam complex
Analyse Crystal structure of CAS-DNA-pam complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DQZ
- Type
- protein + DNA
- Length
- 1,393 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR-associated endonuclease CAS1; DNA (36-mer); CRISPR-associated endoribonuclease CAS2
- EC
- 3.1.-.-
- UniProt
- Q46896, P45956
- Ligands
- MG
- Pockets
- 18 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 46% 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 | CRISPR-associated endonuclease CAS1 (EC 3.1.-.-) | protein | 300 | 46% helix, 14% strand | Q46896 |
| B | CRISPR-associated endonuclease CAS1 (EC 3.1.-.-) | protein | 301 | 47% helix, 14% strand | Q46896 |
| G | DNA (36-mer) | dna | 35 | — | — |
| H | DNA (36-mer) | dna | 35 | — | — |
| F, E | CRISPR-associated endoribonuclease CAS2 (EC 3.1.-.-) | protein | 94 | 23% helix, 46% strand | P45956 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 1004 | 0.86 | 0.87 | 75 | empty |
| 2 | 1177 | 0.84 | 0.85 | 94 | empty |
| 3 | 659 | 0.77 | 0.83 | 44 | empty |
| 4 | 323 | 0.72 | 0.85 | 51 | empty |
| 5 | 286 | 0.71 | 0.85 | 40 | empty |
Interfaces
20 interfaces between chains.
- D–C · 2226 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 2225 Ų buried · 32 hydrogen bonds · protein-protein
- A–G · 1256 Ų buried · 32 hydrogen bonds · protein-nucleic
- D–H · 1248 Ų buried · 34 hydrogen bonds · protein-nucleic
- F–E · 1222 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5DQZ · Crystal Structure of Cas-DNA-PAM 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 F against A, TM-score 0.98
- 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 5DQZ · PDBe 5DQZ · UniProt Q46896 · UniProt P45956
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