Research workbench
60KDA ro autoantigen in complex with a fragment of misfolded RNA
Analyse 60KDA ro autoantigen in complex with a fragment of misfolded RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2I91
- Type
- protein + RNA
- Length
- 1,091 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*GP*CP*CP*UP*AP*CP*CP*C)-3'; 5'- R(*C*GP*GP*UP*AP*GP*GP*CP*UP*UP*UP*UP*CP*AP*A)-3'…
- UniProt
- P42700
- Ligands
- MG
- Pockets
- 11 · best druggability 0.88
Structure
x-ray diffraction · 5 distinct chains · 53% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, E | 5'-R(*GP*CP*CP*UP*AP*CP*CP*C)-3' | rna | 8 | — | — |
| D | 5'- R(*C*GP*GP*UP*AP*GP*GP*CP*UP*UP*UP*UP*CP*AP*A)-3' | rna | 14 | — | — |
| F | 5'- R(*C*GP*GP*UP*AP*GP*GP*CP*UP*UP*UP*UP*CP*AP*A)-3' | rna | 15 | — | — |
| A | 60 kda ss-A/RO ribonucleoprotein | protein | 520 | 53% helix, 9% strand | P42700 |
| B | 60 kda ss-A/RO ribonucleoprotein | protein | 526 | 52% 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
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 929 | 0.88 | 0.90 | 102 | empty |
| 2 | 68 | 0.71 | 0.97 | 18 | empty |
| 3 | 65 | 0.70 | 0.97 | 16 | empty |
| 4 | 360 | 0.70 | 0.83 | 46 | empty |
| 5 | 366 | 0.69 | 0.82 | 47 | empty |
Interfaces
9 interfaces between chains.
- F–B · 1658 Ų buried · 41 hydrogen bonds · protein-nucleic
- D–A · 1655 Ų buried · 43 hydrogen bonds · protein-nucleic
- A–B · 1452 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 443 Ų buried · 43 hydrogen bonds · nucleic-nucleic
- E–F · 435 Ų buried · 43 hydrogen bonds · nucleic-nucleic
Compared structures
- 2I91 · 60kDa Ro autoantigen in complex with a fragment of misfolded RNA · the same entry in another collection · chain B against B, TM-score 1.00
- P42700 · AlphaFold monomer V2.0 prediction for 60 kda ss-A/RO ribonucleoprotein (P42700) · a predicted model of the same protein · chain B against A, TM-score 0.78
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 2I91 · PDBe 2I91 · UniProt P42700
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