Research workbench
Structure of LBCAS12A-crrna complex bound to ACRVA4 (form a complex)
Analyse Structure of LBCAS12A-crrna complex bound to ACRVA4 (form a complex) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KL9
- Type
- protein + RNA
- Length
- 1,439 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LBCAS12A; ACRVA4; RNA (42-mer)
- UniProt
- A0A0U2APF4
- Ligands
- MG
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 3 distinct chains · 40% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LBCAS12A | protein | 1180 | 41% helix, 12% strand | — |
| B, C | ACRVA4 | protein | 117 | 28% helix, 19% strand | A0A0U2APF4 |
| G | RNA (42-mer) | rna | 25 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 458 | 0.80 | 0.88 | 58 | MG |
| 2 | 966 | 0.73 | 0.77 | 92 | empty |
| 3 | 744 | 0.70 | 0.77 | 89 | empty |
| 4 | 125 | 0.69 | 0.90 | 26 | empty |
| 5 | 611 | 0.67 | 0.76 | 43 | empty |
Interfaces
5 interfaces between chains.
- A–G · 2877 Ų buried · 47 hydrogen bonds · protein-nucleic
- A–B · 1488 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 672 Ų buried · 3 hydrogen bonds · protein-protein
- B–G · 179 Ų buried · 5 hydrogen bonds · protein-nucleic
- A–C · 81 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6KL9 · Structure of LbCas12a-crRNA complex bound to AcrVA4 (form A complex) · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 6KL9 · PDBe 6KL9 · UniProt A0A0U2APF4
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