Research workbench
Overall structure of the yeast spliceosome immediately after branching.
Analyse Overall structure of the yeast spliceosome immediately after branching. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LJ5
- Type
- protein + RNA
- Length
- 12,398 residues
- Chains
- 45
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- U5 snrna (small nuclear RNA); Exon 1 (5' exon) of UBC4 pre-mRNA; Intron of UBC4 pre-mRNA…
- EC
- 3.6.4.13, 6.3.2.-
- UniProt
- P33334, P32639, P28320, P53854, P36048, P21374, A0A162ERE7, Q12417, P28004, P25337, Q12046, P38241, Q03654, A0A162GIZ3, Q03375, Q12309, Q04048, P40018, P43321, Q12330, P54999, P40204, Q02260, Q06217, Q08963, P40567, P15938, P32523, Q06091
- Ligands
- GTP, ZN, MG
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 39 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| U | U5 snrna (small nuclear RNA) | rna | 141 | — | — |
| E | Exon 1 (5' exon) of UBC4 pre-mRNA | rna | 16 | — | — |
| I | Intron of UBC4 pre-mRNA | rna | 33 | — | — |
| Z | U2 snrna (small nuclear RNA) | rna | 171 | — | — |
| V | U6 snrna (small nuclear RNA) | rna | 97 | — | — |
| A | Pre-mRNA-splicing factor 8 | protein | 2168 | 43% helix, 13% strand | P33334 |
| B | Pre-mRNA-splicing helicase BRR2 (EC 3.6.4.13) | protein | 1707 | 45% helix, 17% strand | P32639 |
| D | Protein CWC16 | protein | 114 | 11% helix, 32% strand | P28320 |
| F | Pre-mRNA-splicing factor CWC25 | protein | 46 | 74% helix, 0% strand | P53854 |
| C | Pre-mRNA-splicing factor SNU114 | protein | 882 | 36% helix, 17% strand | P36048 |
| G | Pre-mRNA-splicing factor ISY1 | protein | 97 | 60% helix, 1% strand | P21374 |
| H | CWC22 | protein | 399 | 74% helix, 0% strand | A0A162ERE7 |
| J | Pre-mRNA-splicing factor PRP46 | protein | 326 | 3% helix, 42% strand | Q12417 |
| K | Pre-mRNA-processing protein 45 | protein | 163 | 39% helix, 6% strand | P28004 |
| L | Pre-mRNA-splicing factor BUD31 | protein | 155 | 52% helix, 0% strand | P25337 |
| M | Pre-mRNA-splicing factor CWC2 | protein | 252 | 33% helix, 14% strand | Q12046 |
| N | Pre-mRNA-splicing factor SLT11 | protein | 209 | 41% helix, 14% strand | P38241 |
| O | Pre-mRNA-splicing factor CEF1 | protein | 283 | 69% helix, 0% strand | Q03654 |
| P | CWC15 | protein | 36 | 0% helix, 0% strand | A0A162GIZ3 |
| R | Pre-mRNA-splicing factor CWC21 | protein | 97 | 62% helix, 2% strand | Q03375 |
| S | Pre-mRNA-splicing factor CLF1 | protein | 464 | 82% helix, 0% strand | Q12309 |
| T | Pre-mRNA-splicing factor SYF1 | protein | 592 | 81% helix, 0% strand | Q04048 |
| b, k | Small nuclear ribonucleoprotein-associated protein B | protein | 80 | 4% helix, 53% strand | P40018 |
| d, n | Small nuclear ribonucleoprotein sm D3 | protein | 82 | 16% helix, 46% strand | P43321 |
| e, p | Small nuclear ribonucleoprotein E | protein | 75 | 19% helix, 36% strand | Q12330 |
| f, q | Small nuclear ribonucleoprotein F | protein | 72 | 10% helix, 53% strand | P54999 |
| g, r | Small nuclear ribonucleoprotein G | protein | 69 | 0% helix, 48% strand | P40204 |
| h | Small nuclear ribonucleoprotein sm D1 | protein | 82 | 15% helix, 48% strand | Q02260 |
| j, m | Small nuclear ribonucleoprotein sm D2 | protein | 94 | 23% helix, 39% strand | Q06217 |
| W | U2 small nuclear ribonucleoprotein a' | protein | 164 | 21% helix, 5% strand | Q08963 |
| Y | U2 small nuclear ribonucleoprotein B'' | protein | 84 | 26% helix, 18% strand | P40567 |
| l | Small nuclear ribonucleoprotein sm D1 | protein | 79 | 8% helix, 8% strand | Q02260 |
| Q | Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 (EC 3.6.4.13) | protein | 619 | 41% helix, 13% strand | P15938 |
| t | Pre-mRNA-processing factor 19 (EC 6.3.2.-) | protein | 438 | 17% helix, 39% strand | P32523 |
| u | Pre-mRNA-processing factor 19 (EC 6.3.2.-) | protein | 437 | 16% helix, 40% strand | P32523 |
| v | Pre-mRNA-processing factor 19 (EC 6.3.2.-) | protein | 426 | 17% helix, 39% strand | P32523 |
| w | Pre-mRNA-processing factor 19 (EC 6.3.2.-) | protein | 435 | 16% helix, 40% strand | P32523 |
| s | Pre-mRNA-splicing factor SNT309 | protein | 110 | 69% helix, 0% strand | Q06091 |
| x | Unknown | protein | 132 | 92% helix, 0% strand | — |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains C
- ZN · Zinc ion · metal · 7 copies · chains D, L, V, M, N
- MG · Magnesium ion · metal · 2 copies · chains E, I, V
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 893 | 0.89 | 0.92 | 105 | empty |
| 2 | 1035 | 0.89 | 0.90 | 98 | GTP |
| 3 | 912 | 0.88 | 0.91 | 97 | empty |
| 4 | 729 | 0.87 | 0.91 | 92 | empty |
| 5 | 1050 | 0.87 | 0.88 | 90 | empty |
Interfaces
158 interfaces between chains.
- A–C · 4801 Ų buried · 44 hydrogen bonds · protein-protein
- U–A · 3959 Ų buried · 71 hydrogen bonds · protein-nucleic
- A–K · 2199 Ų buried · 11 hydrogen bonds · protein-protein
- Z–A · 1997 Ų buried · 44 hydrogen bonds · protein-nucleic
- A–H · 1910 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5LJ5 · Overall structure of the yeast spliceosome immediately after branching. · the same entry in another collection · chain G against G, 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 P32639
- Every structure of UniProt P28320
- Every structure of UniProt P53854
- Every structure of UniProt P36048
- Every structure of UniProt P21374
- Every structure of UniProt A0A162ERE7
- Every structure of UniProt Q12417
- Every structure of UniProt P28004
- Every structure of UniProt P25337
- Every structure of UniProt Q12046
- Every structure of UniProt P38241
- Every structure of UniProt Q03654
- Every structure of UniProt A0A162GIZ3
- Every structure of UniProt Q03375
- Every structure of UniProt Q12309
- Every structure of UniProt Q04048
- 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
- Every structure of UniProt Q08963
- Every structure of UniProt P40567
- Every structure of UniProt P15938
- Every structure of UniProt P32523
- Every structure of UniProt Q06091
- Elsewhere: RCSB PDB 5LJ5 · PDBe 5LJ5 · UniProt P33334 · UniProt P32639 · UniProt P28320 · UniProt P53854 · UniProt P36048 · UniProt P21374 · UniProt A0A162ERE7 · UniProt Q12417 · UniProt P28004 · UniProt P25337 · UniProt Q12046 · UniProt P38241 · UniProt Q03654 · UniProt A0A162GIZ3 · UniProt Q03375 · UniProt Q12309 · UniProt Q04048 · UniProt P40018 · UniProt P43321 · UniProt Q12330 · UniProt P54999 · UniProt P40204 · UniProt Q02260 · UniProt Q06217 · UniProt Q08963 · UniProt P40567 · UniProt P15938 · UniProt P32523 · UniProt Q06091
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.