MolNFT v1 · #171202 · protein + RNA
Cuta in complex with A3 RNA
6YWO: “Cuta in complex with A3 RNA”. X-ray diffraction, 2 ligands (MG, CL), 16 pockets (best druggability 0.78). MolNFT v1 #171202 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6YWO
- Type
- protein + RNA
- Length
- 1,416 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cuta; RNA (5'-R(*AP*AP*A)-3')
- UniProt
- G2R014
- Ligands
- MG, CL
- Pockets
- 16 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cuta | protein | 354 | 47% helix, 12% strand | G2R014 |
| B | Cuta | protein | 353 | 47% helix, 12% strand | G2R014 |
| C | Cuta | protein | 347 | 48% helix, 12% strand | G2R014 |
| D | Cuta | protein | 350 | 47% helix, 12% strand | G2R014 |
| E, I, F, K | RNA (5'-R(*AP*AP*A)-3') | rna | 3 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 12 copies · chains A, F, B, E, C, I, D, K
- CL · Chloride ion · ion · 2 copies · chains A, F, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1121 | 0.78 | 0.80 | 81 | empty |
| 2 | 1016 | 0.76 | 0.79 | 75 | empty |
| 3 | 239 | 0.71 | 0.87 | 26 | empty |
| 4 | 339 | 0.62 | 0.78 | 32 | MG |
| 5 | 333 | 0.60 | 0.78 | 43 | empty |
Interfaces
11 interfaces between chains.
- A–C · 1067 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 971 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 732 Ų buried · 7 hydrogen bonds · protein-protein
- B–E · 611 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–F · 608 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 40 modified, 4 disulfide (engineered, disulfide).
Compared structures
- 6YWO · CutA in complex with A3 RNA · 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 G2R014
- Elsewhere: RCSB PDB 6YWO · PDBe 6YWO · UniProt G2R014
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