MolNFT v1 · #150430 · protein + DNA + RNA
Transition state structure of CPF1(CAS12A) I4 conformation
6GTG · CRISPR-associated endonuclease CAS12A: “Transition state structure of CPF1(CAS12A) I4 conformation”. Electron microscopy, 1 ligand (MG), 20 pockets (best druggability 0.80). MolNFT v1 #150430 on GenesisL1: 3D structure, binding…
- PDB
- 6GTG
- Type
- protein + DNA + RNA
- Length
- 1,389 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR-associated endonuclease CAS12A; RNA (40-mer); DNA (32-mer); DNA (5'…
- EC
- 3.1.21.1, 3.1.27.2
- UniProt
- A0Q7Q2
- Ligands
- MG
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 4 distinct chains · 31% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated endonuclease CAS12A (EC 3.1.21.1, 3.1.27.2) | protein | 1298 | 31% helix, 8% strand | A0Q7Q2 |
| B | RNA (40-mer) | rna | 41 | — | — |
| C | DNA (32-mer) | dna | 32 | — | — |
| D | DNA (5'- D(P*CP*GP*AP*GP*CP*TP*CP*GP*TP*TP*AP*GP*AP*GP*AP*AP*GP*T)-3') | dna | 18 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 518 | 0.80 | 0.87 | 56 | empty |
| 2 | 1035 | 0.80 | 0.82 | 65 | empty |
| 3 | 840 | 0.76 | 0.80 | 52 | empty |
| 4 | 858 | 0.74 | 0.79 | 61 | empty |
| 5 | 54 | 0.73 | 0.98 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–B · 4377 Ų buried · 76 hydrogen bonds · protein-nucleic
- A–C · 2747 Ų buried · 37 hydrogen bonds · protein-nucleic
- A–D · 1196 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–C · 902 Ų buried · 69 hydrogen bonds · nucleic-nucleic
- C–D · 513 Ų buried · 47 hydrogen bonds · nucleic-nucleic
Compared structures
- 6GTG · Transition state structure of Cpf1(Cas12a) I4 conformation · the same entry in another collection · chain A against A, TM-score 1.00
- A0Q7Q2 · AlphaFold monomer V2.0 prediction for CRISPR-associated endonuclease CAS12A (A0Q7Q2) · a predicted model of the same protein · chain A 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 A0Q7Q2
- Elsewhere: RCSB PDB 6GTG · PDBe 6GTG · UniProt A0Q7Q2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.