MolNFT v1 · #150969 · protein + RNA
CSF5, CRISPR-CAS type IV CAS6 crrna endonuclease
6H9I: “CSF5, CRISPR-CAS type IV CAS6 crrna endonuclease”. X-ray diffraction, 1 ligand (MN), 12 pockets (best druggability 0.56). MolNFT v1 #150969 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6H9I
- Type
- protein + RNA
- Length
- 550 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CSF5; Crrna
- UniProt
- Q5NWP0
- Ligands
- MN
- Pockets
- 12 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | CSF5 | protein | 250 | 30% helix, 36% strand | Q5NWP0 |
| C, E | Crrna | rna | 25 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · chains B
- TLA · L(+)-tartaric acid · additive · 3 copies · chains A, C, B, E
- GOL · Glycerol · additive · 3 copies · chains A, C, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 362 | 0.56 | 0.75 | 39 | empty |
| 2 | 159 | 0.52 | 0.79 | 20 | empty |
| 3 | 208 | 0.50 | 0.76 | 25 | empty |
| 4 | 209 | 0.48 | 0.76 | 29 | empty |
| 5 | 79 | 0.44 | 0.82 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–C · 2153 Ų buried · 82 hydrogen bonds · protein-nucleic
- B–E · 2143 Ų buried · 83 hydrogen bonds · protein-nucleic
- A–B · 262 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 138 Ų buried · 3 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6H9I · Csf5, CRISPR-Cas type IV Cas6 crRNA endonuclease · 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 Q5NWP0
- Elsewhere: RCSB PDB 6H9I · PDBe 6H9I · UniProt Q5NWP0
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