Research workbench
CSF5, CRISPR-CAS type IV CAS6 crrna endonuclease
Analyse CSF5, CRISPR-CAS type IV CAS6 crrna endonuclease in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H9H
- Type
- protein + RNA
- Length
- 547 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CSF5; Crrna
- UniProt
- Q5NWP0
- Ligands
- MN
- Pockets
- 13 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | CSF5 | protein | 250 | 30% helix, 36% strand | Q5NWP0 |
| D | Crrna | rna | 23 | — | — |
| E | Crrna | rna | 24 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · chains B, A
- TLA · L(+)-tartaric acid · additive · 4 copies · chains A, D, B, E
- GOL · Glycerol · additive · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.54 | 0.88 | 20 | GOL |
| 2 | 166 | 0.49 | 0.78 | 26 | TLA |
| 3 | 186 | 0.48 | 0.76 | 29 | empty |
| 4 | 124 | 0.47 | 0.79 | 17 | empty |
| 5 | 100 | 0.43 | 0.78 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–D · 2179 Ų buried · 67 hydrogen bonds · protein-nucleic
- B–E · 2167 Ų buried · 67 hydrogen bonds · protein-nucleic
- B–A · 410 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6H9H · Csf5, CRISPR-Cas type IV Cas6 crRNA endonuclease · the same entry in another collection · chain B against B, 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 Q5NWP0
- Elsewhere: RCSB PDB 6H9H · PDBe 6H9H · UniProt Q5NWP0
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