MolNFT v1 · #126038 · protein + RNA
Yeast activated spliceosome
5LQW · Pre-mRNA-splicing factor 8: “Yeast activated spliceosome”. Electron microscopy, 20 pockets (best druggability 0.72). MolNFT v1 #126038 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5LQW
- Type
- protein + RNA
- Length
- 10,718 residues
- Chains
- 31
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pre-mRNA-splicing factor 8; Pre-mRNA-splicing factor SNU114; Pre-mRNA-splicing helicase…
- EC
- 3.6.4.13
- UniProt
- P33334, P36048, P32639, P38241, P25337, Q12046, P53333, P40565, Q12417, P46947, P28004, Q07930, P20095, Q04048, P49955, Q12309, Q03654, Q04693, Q06835, P0C074, P40018, P43321, Q12330, P54999, P40204, Q02260, Q06217
- Pockets
- 20 · best druggability 0.72
Structure
electron microscopy · 31 distinct chains · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pre-mRNA-splicing factor 8 | protein | 2130 | 0% helix, 0% strand | P33334 |
| B | Pre-mRNA-splicing factor SNU114 | protein | 843 | 0% helix, 0% strand | P36048 |
| C | Pre-mRNA-splicing helicase BRR2 (EC 3.6.4.13) | protein | 1811 | 0% helix, 0% strand | P32639 |
| D | Pre-mRNA-splicing factor SLT11 | protein | 187 | 0% helix, 0% strand | P38241 |
| E | Pre-mRNA-splicing factor BUD31 | protein | 138 | 0% helix, 0% strand | P25337 |
| F | Pre-mRNA-splicing factor CWC2 | protein | 218 | 0% helix, 0% strand | Q12046 |
| H | Pre-mRNA-splicing factor CWC22 | protein | 437 | 0% helix, 0% strand | P53333 |
| J | U2 snrnp component IST3 | protein | 104 | 0% helix, 0% strand | P40565 |
| K | Pre-mRNA-splicing factor PRP46 | protein | 338 | 0% helix, 0% strand | Q12417 |
| L | Pre-mRNA-splicing factor CWC26 | protein | 32 | 0% helix, 0% strand | P46947 |
| M | Pre-mRNA-processing protein 45 | protein | 169 | 0% helix, 0% strand | P28004 |
| N | Pre-mRNA leakage protein 1 | protein | 159 | 0% helix, 0% strand | Q07930 |
| O | Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2 (EC 3.6.4.13) | protein | 628 | 0% helix, 0% strand | P20095 |
| P | Pre-mRNA-splicing factor SYF1 | protein | 202 | 0% helix, 0% strand | Q04048 |
| Q | U2 snrnp component HSH155 | protein | 791 | 0% helix, 0% strand | P49955 |
| R | Pre-mRNA-splicing factor CLF1 | protein | 219 | 0% helix, 0% strand | Q12309 |
| W | Pre-mRNA-splicing factor CEF1 | protein | 128 | 0% helix, 0% strand | Q03654 |
| X | Pre-mRNA-splicing factor RSE1 | protein | 1095 | 0% helix, 0% strand | Q04693 |
| Y | Pre-mRNA-splicing factor RDS3 | protein | 89 | 0% helix, 0% strand | Q06835 |
| Z | RDS3 complex subunit 10 | protein | 68 | 0% helix, 0% strand | P0C074 |
| b | Small nuclear ribonucleoprotein-associated protein B | protein | 80 | 0% helix, 0% strand | P40018 |
| d | Small nuclear ribonucleoprotein sm D3 | protein | 82 | 0% helix, 0% strand | P43321 |
| e | Small nuclear ribonucleoprotein E | protein | 75 | 0% helix, 0% strand | Q12330 |
| f | Small nuclear ribonucleoprotein F | protein | 72 | 0% helix, 0% strand | P54999 |
| g | Small nuclear ribonucleoprotein G | protein | 69 | 0% helix, 0% strand | P40204 |
| h | Small nuclear ribonucleoprotein sm D1 | protein | 82 | 0% helix, 0% strand | Q02260 |
| j | Small nuclear ribonucleoprotein sm D2 | protein | 94 | 0% helix, 0% strand | Q06217 |
| 2 | U2 snrna | rna | 81 | — | — |
| 5 | U5 snrna | rna | 141 | — | — |
| 6 | U6 snrna | rna | 102 | — | — |
| 9 | Actin pre-mRNA | rna | 54 | — | — |
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 643 | 0.72 | 0.80 | 65 | empty |
| 2 | 644 | 0.70 | 0.79 | 30 | empty |
| 3 | 1137 | 0.70 | 0.75 | 67 | empty |
| 4 | 363 | 0.64 | 0.80 | 37 | empty |
| 5 | 242 | 0.61 | 0.81 | 26 | empty |
Interfaces
65 interfaces between chains.
- A–5 · 1295 Ų buried · 0 hydrogen bonds · protein-nucleic
- 2–6 · 1181 Ų buried · 52 hydrogen bonds · nucleic-nucleic
- A–6 · 742 Ų buried · 0 hydrogen bonds · protein-nucleic
- F–6 · 675 Ų buried · 0 hydrogen bonds · protein-nucleic
- E–6 · 607 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 5LQW · yeast activated spliceosome · the same entry in another collection · chain M against M, 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 P36048
- Every structure of UniProt P32639
- Every structure of UniProt P38241
- Every structure of UniProt P25337
- Every structure of UniProt Q12046
- Every structure of UniProt P53333
- Every structure of UniProt P40565
- Every structure of UniProt Q12417
- Every structure of UniProt P46947
- Every structure of UniProt P28004
- Every structure of UniProt Q07930
- Every structure of UniProt P20095
- Every structure of UniProt Q04048
- Every structure of UniProt P49955
- Every structure of UniProt Q12309
- Every structure of UniProt Q03654
- Every structure of UniProt Q04693
- Every structure of UniProt Q06835
- Every structure of UniProt P0C074
- Every structure of UniProt P40018
- Every structure of UniProt P43321
- Every structure of UniProt Q12330
- Every structure of UniProt P54999
- Every structure of UniProt P40204
- Every structure of UniProt Q02260
- Every structure of UniProt Q06217
- Elsewhere: RCSB PDB 5LQW · PDBe 5LQW · UniProt P33334 · UniProt P36048 · UniProt P32639 · UniProt P38241 · UniProt P25337 · UniProt Q12046 · UniProt P53333 · UniProt P40565 · UniProt Q12417 · UniProt P46947 · UniProt P28004 · UniProt Q07930 · UniProt P20095 · UniProt Q04048 · UniProt P49955 · UniProt Q12309 · UniProt Q03654 · UniProt Q04693 · UniProt Q06835 · UniProt P0C074 · UniProt P40018 · UniProt P43321 · UniProt Q12330 · UniProt P54999 · UniProt P40204 · UniProt Q02260 · UniProt Q06217
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