Research workbench
Ro autoantigen complexed with rnas
Analyse Ro autoantigen complexed with rnas in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YVP
- Type
- protein + RNA
- Length
- 1,113 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Y RNA sequence, first strand; Y RNA sequence, second strand; 60-kda ss-A/RO…
- UniProt
- P42700
- Ligands
- MG
- Pockets
- 15 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 53% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, E | Y RNA sequence, first strand | rna | 10 | — | — |
| D, F | Y RNA sequence, second strand | rna | 10 | — | — |
| G | Y RNA sequence, first strand | rna | 5 | — | — |
| H | Y RNA sequence, first strand | rna | 7 | — | — |
| A | 60-kda ss-A/RO ribonucleoprotein | protein | 529 | 54% helix, 9% strand | P42700 |
| B | 60-kda ss-A/RO ribonucleoprotein | protein | 532 | 53% helix, 9% strand | P42700 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 993 | 0.77 | 0.79 | 65 | ACT |
| 2 | 600 | 0.72 | 0.80 | 43 | empty |
| 3 | 374 | 0.65 | 0.79 | 43 | empty |
| 4 | 264 | 0.52 | 0.75 | 28 | empty |
| 5 | 195 | 0.51 | 0.77 | 26 | empty |
Interfaces
10 interfaces between chains.
- H–B · 1010 Ų buried · 24 hydrogen bonds · protein-nucleic
- G–A · 902 Ų buried · 20 hydrogen bonds · protein-nucleic
- E–B · 780 Ų buried · 25 hydrogen bonds · protein-nucleic
- C–A · 775 Ų buried · 27 hydrogen bonds · protein-nucleic
- F–B · 472 Ų buried · 13 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 8 modified (nucleotide modification).
Compared structures
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 P42700
- Elsewhere: RCSB PDB 1YVP · PDBe 1YVP · UniProt P42700
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