Research workbench
Crystal structure of a yeast SNU114-PRP8 complex
Analyse Crystal structure of a yeast SNU114-PRP8 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TEO
- Type
- protein
- Length
- 2,019 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pre-mRNA-splicing factor SNU114; Pre-mRNA-splicing factor 8
- UniProt
- P36048, P33334
- Ligands
- GTP, MG, SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pre-mRNA-splicing factor SNU114 | protein | 863 | 40% helix, 23% strand | P36048 |
| B | Pre-mRNA-splicing factor 8 | protein | 148 | 26% helix, 1% strand | P33334 |
| C | Pre-mRNA-splicing factor SNU114 | protein | 867 | 40% helix, 22% strand | P36048 |
| D | Pre-mRNA-splicing factor 8 | protein | 141 | 28% helix, 1% strand | P33334 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 937 | 0.81 | 0.82 | 108 | GTP |
| 2 | 1051 | 0.80 | 0.81 | 109 | GTP, MG |
| 3 | 450 | 0.76 | 0.85 | 66 | empty |
| 4 | 1096 | 0.74 | 0.77 | 91 | SO4 |
| 5 | 406 | 0.70 | 0.82 | 59 | empty |
Interfaces
5 interfaces between chains.
- A–B · 5288 Ų buried · 54 hydrogen bonds · protein-protein
- C–D · 5179 Ų buried · 53 hydrogen bonds · protein-protein
- A–C · 942 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 308 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 117 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
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 P36048
- Every structure of UniProt P33334
- Elsewhere: RCSB PDB 6TEO · PDBe 6TEO · UniProt P36048 · UniProt P33334
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.