Research workbench
Symmetrical pam-pam prespacer bound CAS4/CAS1/CAS2 complex
Analyse Symmetrical pam-pam prespacer bound CAS4/CAS1/CAS2 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MI4
- Type
- protein + DNA
- Length
- 2,048 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR-associated exonuclease CAS4/ENDONUCLEASE CAS1 fusion; CRISPR-associated…
- EC
- 3.1.-.-, 3.1.12.1
- UniProt
- Q74H36, Q74H35
- Ligands
- SF4, MN
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | CRISPR-associated exonuclease CAS4/ENDONUCLEASE CAS1 fusion (EC 3.1.-.-, 3.1.12.1) | protein | 554 | 44% helix, 17% strand | Q74H36 |
| B, D | CRISPR-associated exonuclease CAS4/ENDONUCLEASE CAS1 fusion (EC 3.1.-.-, 3.1.12.1) | protein | 340 | 48% helix, 14% strand | Q74H36 |
| E, F | CRISPR-associated endoribonuclease CAS2 (EC 3.1.-.-) | protein | 95 | 28% helix, 32% strand | Q74H35 |
| G, H | DNA (35-mer) | dna | 35 | — | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, C
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, G, D, E, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1063 | 0.83 | 0.84 | 114 | empty |
| 2 | 842 | 0.83 | 0.85 | 97 | MN |
| 3 | 549 | 0.82 | 0.88 | 72 | empty |
| 4 | 543 | 0.80 | 0.86 | 67 | empty |
| 5 | 346 | 0.69 | 0.83 | 27 | empty |
Interfaces
18 interfaces between chains.
- C–D · 2378 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 2349 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 1399 Ų buried · 19 hydrogen bonds · protein-protein
- C–G · 1138 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–H · 1135 Ų buried · 23 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7MI4 · Symmetrical PAM-PAM prespacer bound Cas4/Cas1/Cas2 complex · the same entry in another collection · chain H against H, TM-score 1.00
- Q74H36 · AlphaFold monomer V2.0 prediction for CRISPR-associated exonuclease CAS4/ENDONUCLEASE… · a predicted model of the same protein · chain A against A, TM-score 0.97
- Q74H35 · AlphaFold monomer V2.0 prediction for CRISPR-associated endoribonuclease CAS2 (Q74H35) · a predicted model of the same protein · chain E against A, TM-score 0.86
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 Q74H36
- Every structure of UniProt Q74H35
- Elsewhere: RCSB PDB 7MI4 · PDBe 7MI4 · UniProt Q74H36 · UniProt Q74H35
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