Research workbench
Body region of the U4/U6.U5 tri-snrnp
Analyse Body region of the U4/U6.U5 tri-snrnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GAP
- Type
- protein + RNA
- Length
- 3,728 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- U4 snrna, 5' region, nucleotides 1-67; U6 snrna; U5 snrna; Unknown protein…
- EC
- 3.6.4.13
- UniProt
- P33334, P20053, P19735, Q06819, P49704, Q03338, P39990, P32639
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 12 distinct chains · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| V | U4 snrna, 5' region, nucleotides 1-67 | rna | 67 | — | — |
| W | U6 snrna | rna | 56 | — | — |
| U | U5 snrna | rna | 20 | — | — |
| x | Unknown protein | protein | 82 | 61% helix, 2% strand | — |
| A | Pre-mRNA-splicing factor 8 | protein | 1349 | 49% helix, 13% strand | P33334 |
| H | U4/U6 small nuclear ribonucleoprotein PRP4 | protein | 357 | 13% helix, 40% strand | P20053 |
| J | Pre-mRNA-splicing factor 6 | protein | 729 | 71% helix, 0% strand | P19735 |
| D | Spliceosomal protein DIB1 | protein | 140 | 31% helix, 18% strand | Q06819 |
| F | Pre-mRNA-processing factor 31 | protein | 415 | 60% helix, 2% strand | P49704 |
| G | U4/U6 small nuclear ribonucleoprotein PRP3 | protein | 318 | 41% helix, 12% strand | Q03338 |
| K | 13 kda ribonucleoprotein-associated protein | protein | 124 | 49% helix, 15% strand | P39990 |
| B | Pre-mRNA-splicing helicase BRR2 (EC 3.6.4.13) | protein | 71 | 63% helix, 0% strand | P32639 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 945 | 0.86 | 0.88 | 86 | empty |
| 2 | 1023 | 0.85 | 0.86 | 91 | empty |
| 3 | 1027 | 0.84 | 0.85 | 96 | empty |
| 4 | 998 | 0.83 | 0.84 | 102 | empty |
| 5 | 876 | 0.80 | 0.83 | 103 | empty |
Interfaces
35 interfaces between chains.
- A–F · 4114 Ų buried · 36 hydrogen bonds · protein-protein
- A–J · 3055 Ų buried · 28 hydrogen bonds · protein-protein
- H–G · 2957 Ų buried · 20 hydrogen bonds · protein-protein
- J–F · 2122 Ų buried · 17 hydrogen bonds · protein-protein
- V–F · 1965 Ų buried · 38 hydrogen bonds · protein-nucleic
Compared structures
- 5GAP · Body region of the U4/U6.U5 tri-snRNP · the same entry in another collection · chain B against B, 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 P33334
- Every structure of UniProt P20053
- Every structure of UniProt P19735
- Every structure of UniProt Q06819
- Every structure of UniProt P49704
- Every structure of UniProt Q03338
- Every structure of UniProt P39990
- Every structure of UniProt P32639
- Elsewhere: RCSB PDB 5GAP · PDBe 5GAP · UniProt P33334 · UniProt P20053 · UniProt P19735 · UniProt Q06819 · UniProt P49704 · UniProt Q03338 · UniProt P39990 · UniProt P32639
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