MolNFT v1 · #146811 · protein + RNA
High-resolution crystal structure of CAS13B from prevotella buccae
6DTD · Nuclease: “High-resolution crystal structure of CAS13B from prevotella buccae”. X-ray diffraction, 2 ligands (NA, CL), 12 pockets (best druggability 0.88). MolNFT v1 #146811 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6DTD
- Type
- protein + RNA
- Length
- 1,090 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclease; RNA (37-mer)
- EC
- 3.1.-.-
- UniProt
- E6K398
- Ligands
- NA, CL
- Pockets
- 12 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclease (EC 3.1.-.-) | protein | 1053 | 54% helix, 9% strand | E6K398 |
| C | RNA (37-mer) | rna | 37 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains C
- CL · Chloride ion · ion · 2 copies · chains A, C
- CIT · Citric acid · additive · 7 copies · chains A, C
- PG4 · Tetraethylene glycol · additive · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1016 | 0.88 | 0.90 | 92 | CL, NA |
| 2 | 883 | 0.78 | 0.81 | 97 | empty |
| 3 | 208 | 0.54 | 0.78 | 29 | empty |
| 4 | 292 | 0.52 | 0.74 | 31 | CIT |
| 5 | 121 | 0.47 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–C · 3524 Ų buried · 90 hydrogen bonds · protein-nucleic
Compared structures
- 6DTD · High-resolution crystal structure of Cas13b from Prevotella buccae · 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 E6K398
- Elsewhere: RCSB PDB 6DTD · PDBe 6DTD · UniProt E6K398
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