Research workbench
The crystal structure of a binary U5 snrnp complex
Analyse The crystal structure of a binary U5 snrnp complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SYX
- Type
- protein
- Length
- 591 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spliceosomal U5 snrnp-specific 15 kda protein; CD2 antigen cytoplasmic tail-binding…
- UniProt
- P83876, O95400
- Pockets
- 6 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Spliceosomal U5 snrnp-specific 15 kda protein | protein | 135 | 33% helix, 24% strand | P83876 |
| B, D, F | CD2 antigen cytoplasmic tail-binding protein 2 | protein | 62 | 26% helix, 26% strand | O95400 |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.57 | 0.84 | 34 | empty |
| 2 | 62 | 0.54 | 0.88 | 21 | empty |
| 3 | 94 | 0.36 | 0.75 | 16 | empty |
| 4 | 74 | 0.33 | 0.75 | 16 | empty |
| 5 | 69 | 0.32 | 0.75 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–B · 693 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 682 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 672 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 378 Ų buried · 4 hydrogen bonds · protein-protein
- C–F · 236 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1SYX · The crystal structure of a binary U5 snRNP complex · the same entry in another collection · chain F against F, TM-score 1.00
- P83876 · AlphaFold monomer V2.0 prediction for thioredoxin-like protein 4A (P83876) · a predicted model of the same protein · chain A against A, TM-score 0.99
- O95400 · AlphaFold monomer V2.0 prediction for CD2 antigen cytoplasmic tail- binding protein 2… · a predicted model of the same protein · chain F against A, TM-score 0.96
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 P83876
- Every structure of UniProt O95400
- Elsewhere: RCSB PDB 1SYX · PDBe 1SYX · UniProt P83876 · UniProt O95400
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