MolNFT v1 · #159350 · protein + DNA + RNA
Cryoem structure of the LBCAS12A-crrna-ACRVA4-DNA complex
6OMV · DNA (5'- D(P*TP*AP*AP*TP*TP*TP*CP*CP*TP*AP*AP*AP*GP*GP*AP*CP…: “Cryoem structure of the LBCAS12A-crrna-ACRVA4-DNA complex”. Electron microscopy, 1 ligand (MG), 20 pockets (best druggability 0.83). MolNFT v1 #159350 on GenesisL1: 3D…
- PDB
- 6OMV
- Type
- protein + DNA + RNA
- Length
- 1,495 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(P*TP*AP*AP*TP*TP*TP*CP*CP*TP*AP*AP*AP*GP*GP*AP*CP*G)-3'); DNA…
- UniProt
- A0A0U2APF4, A0A182DWE3
- Ligands
- MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 6 distinct chains · 39% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | DNA (5'- D(P*TP*AP*AP*TP*TP*TP*CP*CP*TP*AP*AP*AP*GP*GP*AP*CP*G)-3') | dna | 17 | — | — |
| F | DNA (5'-D(*CP*GP*TP*CP*CP*TP*TP*TP*AP*GP*GP*A)-3') | dna | 12 | — | — |
| A | ACRVA4 | protein | 115 | 31% helix, 21% strand | A0A0U2APF4 |
| B | CPF1 | protein | 1208 | 40% helix, 12% strand | A0A182DWE3 |
| G | RNA | rna | 29 | — | — |
| C | ACRVA4 | protein | 114 | 31% helix, 17% strand | A0A0U2APF4 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, G, 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 840 | 0.83 | 0.85 | 66 | empty |
| 2 | 986 | 0.75 | 0.78 | 89 | empty |
| 3 | 1090 | 0.74 | 0.77 | 82 | empty |
| 4 | 283 | 0.73 | 0.87 | 46 | MG |
| 5 | 258 | 0.57 | 0.78 | 44 | empty |
Interfaces
9 interfaces between chains.
- B–G · 3156 Ų buried · 62 hydrogen bonds · protein-nucleic
- A–B · 1478 Ų buried · 11 hydrogen bonds · protein-protein
- E–B · 1163 Ų buried · 22 hydrogen bonds · protein-nucleic
- F–B · 1005 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–C · 785 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6OMV · CryoEM structure of the LbCas12a-crRNA-AcrVA4-DNA complex · the same entry in another collection · chain E against E, TM-score 1.00
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 A0A0U2APF4
- Every structure of UniProt A0A182DWE3
- Elsewhere: RCSB PDB 6OMV · PDBe 6OMV · UniProt A0A0U2APF4 · UniProt A0A182DWE3
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