MolNFT v1 · #182150 · protein + DNA
Sub-complex of CAS4-CAS1-CAS2 bound pam containing DNA
7MID · CRISPR-associated exonuclease CAS4/ENDONUCLEASE CAS1 fusion: “Sub-complex of CAS4-CAS1-CAS2 bound pam containing DNA”. Electron microscopy, 2 ligands (SF4, MN), 19 pockets (best druggability 0.82). MolNFT v1 #182150 on GenesisL1: 3D…
- PDB
- 7MID
- Type
- protein + DNA
- Length
- 1,137 residues
- Chains
- 6
- 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
- 19 · best druggability 0.82
Structure
electron microscopy · 6 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated exonuclease CAS4/ENDONUCLEASE CAS1 fusion (EC 3.1.-.-, 3.1.12.1) | protein | 554 | 44% helix, 17% strand | Q74H36 |
| B | CRISPR-associated exonuclease CAS4/ENDONUCLEASE CAS1 fusion (EC 3.1.-.-, 3.1.12.1) | protein | 340 | 48% helix, 14% strand | Q74H36 |
| C | CRISPR-associated endoribonuclease CAS2 (EC 3.1.-.-) | protein | 95 | 28% helix, 32% strand | Q74H35 |
| D | CRISPR-associated endoribonuclease CAS2 (EC 3.1.-.-) | protein | 91 | 30% helix, 32% strand | Q74H35 |
| E | DNA (5'- D(P*CP*AP*CP*CP*AP*TP*CP*GP*TP*GP*AP*GP*GP*CP*CP*TP*CP*AP*GP*CP*TP*AP *CP*G)-3') | dna | 24 | — | — |
| F | DNA (33-mer) | dna | 33 | — | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains A
- MN · Manganese (II) ion · metal · 5 copies · chains A, B, C, F, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 745 | 0.82 | 0.86 | 90 | empty |
| 2 | 900 | 0.82 | 0.84 | 92 | empty |
| 3 | 440 | 0.70 | 0.81 | 35 | empty |
| 4 | 53 | 0.68 | 0.97 | 17 | empty |
| 5 | 446 | 0.67 | 0.79 | 48 | MN |
Interfaces
12 interfaces between chains.
- A–B · 2355 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1415 Ų buried · 19 hydrogen bonds · protein-protein
- A–F · 1136 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–C · 1133 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 1009 Ų buried · 87 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7MID · Sub-complex of Cas4-Cas1-Cas2 bound PAM containing DNA · the same entry in another collection · chain F against F, 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 D against A, TM-score 0.88
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 7MID · PDBe 7MID · UniProt Q74H36 · UniProt Q74H35
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