MolNFT v1 · #153429 · protein + DNA + RNA
Crystal structure of NME1CAS9-sgrna-dsdna dimer mediated by double protein inhibitor ACRIIC3 monomers
6JE4 · CRISPR-associated endonuclease CAS9: “Crystal structure of NME1CAS9-sgrna-dsdna dimer mediated by double protein inhibitor ACRIIC3 monomers”. X-ray diffraction, 20 pockets (best druggability 0.88). MolNFT v1 #153429 on GenesisL1: 3D…
- PDB
- 6JE4
- Type
- protein + DNA + RNA
- Length
- 5,418 residues
- Chains
- 20
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR-associated endonuclease CAS9; Target DNA strand; Non-target DNA strand; Sgrna…
- EC
- 3.1.-.-
- UniProt
- C9X1G5, A0A3E2QDI5
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 11 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated endonuclease CAS9 (EC 3.1.-.-) | protein | 1049 | 41% helix, 16% strand | C9X1G5 |
| C, G, M, Q | Target DNA strand | dna | 35 | — | — |
| D | Non-target DNA strand | dna | 15 | — | — |
| B, F | Sgrna | rna | 132 | — | — |
| I, J, S, T | ACRIIC3 | protein | 117 | 42% helix, 27% strand | A0A3E2QDI5 |
| E | CRISPR-associated endonuclease CAS9 (EC 3.1.-.-) | protein | 1056 | 40% helix, 16% strand | C9X1G5 |
| H, N, R | Non-target DNA strand | dna | 18 | — | — |
| K | CRISPR-associated endonuclease CAS9 (EC 3.1.-.-) | protein | 1060 | 40% helix, 16% strand | C9X1G5 |
| L | Sgrna | rna | 133 | — | — |
| O | CRISPR-associated endonuclease CAS9 (EC 3.1.-.-) | protein | 1049 | 40% helix, 16% strand | C9X1G5 |
| P | Sgrna | rna | 130 | — | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 18 copies · chains A, B, E, G, F, J, K, L, M, O, P
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains B, F, K
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 | 1116 | 0.88 | 0.90 | 98 | EDO |
| 2 | 679 | 0.86 | 0.91 | 61 | empty |
| 3 | 620 | 0.85 | 0.91 | 52 | empty |
| 4 | 574 | 0.85 | 0.91 | 49 | empty |
| 5 | 533 | 0.83 | 0.90 | 59 | EDO |
Interfaces
33 interfaces between chains.
- K–L · 6599 Ų buried · 155 hydrogen bonds · protein-nucleic
- E–F · 6559 Ų buried · 154 hydrogen bonds · protein-nucleic
- O–P · 6475 Ų buried · 146 hydrogen bonds · protein-nucleic
- A–B · 6470 Ų buried · 150 hydrogen bonds · protein-nucleic
- A–C · 2143 Ų buried · 38 hydrogen bonds · protein-nucleic
Compared structures
- 6JE4 · Crystal structure of Nme1Cas9-sgRNA-dsDNA dimer mediated by double protein inhibitor… · the same entry in another collection · chain T against T, 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 C9X1G5
- Every structure of UniProt A0A3E2QDI5
- Elsewhere: RCSB PDB 6JE4 · PDBe 6JE4 · UniProt C9X1G5 · UniProt A0A3E2QDI5
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