Research workbench
Structure of the SPCAS9 DNA adenine base editor - ABE8E
Analyse Structure of the SPCAS9 DNA adenine base editor - ABE8E in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VPC
- Type
- protein + DNA + RNA
- Length
- 1,786 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CAS9 (SPCAS9) single-guide RNA (sgrna); CRISPR-associated endonuclease CAS9; DNA target…
- EC
- 3.1.-.-
- UniProt
- A0A4U7H5M9
- Ligands
- MG, ZN
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 6 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CAS9 (SPCAS9) single-guide RNA (sgrna) | rna | 81 | — | — |
| B | CRISPR-associated endonuclease CAS9 (EC 3.1.-.-) | protein | 1332 | 48% helix, 12% strand | A0A4U7H5M9 |
| C | DNA target strand (ts) | dna | 40 | — | — |
| D | DNA non-target strand (nts) | dna | 32 | — | — |
| E | T-RNA adenine deaminase a V8E (tada-8E) | protein | 145 | 38% helix, 19% strand | — |
| F | T-RNA adenine deaminase a V8E (tada-8E) | protein | 156 | 40% helix, 17% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains E, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1127 | 0.84 | 0.85 | 98 | MG |
| 2 | 1001 | 0.81 | 0.82 | 78 | empty |
| 3 | 993 | 0.77 | 0.79 | 77 | empty |
| 4 | 628 | 0.71 | 0.79 | 56 | empty |
| 5 | 335 | 0.71 | 0.83 | 36 | ZN |
Interfaces
10 interfaces between chains.
- A–B · 5667 Ų buried · 95 hydrogen bonds · protein-nucleic
- B–C · 1475 Ų buried · 14 hydrogen bonds · protein-nucleic
- E–F · 1246 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 1154 Ų buried · 13 hydrogen bonds · protein-nucleic
- C–D · 983 Ų buried · 57 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6VPC · Structure of the SpCas9 DNA adenine base editor - ABE8e · 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 A0A4U7H5M9
- Elsewhere: RCSB PDB 6VPC · PDBe 6VPC · UniProt A0A4U7H5M9
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