MolNFT v1 · #127212 · protein + RNA
Structure of a spliceosome remodeled for exon ligation
5MPS · Yeast UBC4 gene for ubiquitin-conjugating enzyme: “Structure of a spliceosome remodeled for exon ligation”. Electron microscopy, 5 ligands (IHP, GTP, ZN), 20 pockets (best druggability 0.89). MolNFT v1 #127212 on GenesisL1: 3D…
- PDB
- 5MPS
- Type
- protein + RNA
- Length
- 7,143 residues
- Chains
- 30
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yeast UBC4 gene for ubiquitin-conjugating enzyme; UBC4 gene exon; U2 snrna; Saccharomyces…
- UniProt
- P33334, P36048, P53333, Q12417, P28004, P25337, Q12046, P38241, Q03654, Q03772, Q03375, Q12309, Q04048, P33411, Q02775, P40968, P53277, P40018, P43321, Q12330, P54999, P40204, Q02260, Q06217
- Ligands
- IHP, GTP, ZN, MG, K
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 30 distinct chains · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I | Yeast UBC4 gene for ubiquitin-conjugating enzyme | rna | 34 | — | — |
| E | UBC4 gene exon | rna | 16 | — | — |
| 2 | U2 snrna | rna | 49 | — | — |
| 6 | Saccharomyces cerevisiae strain T.52_2H chromosome XII sequence | rna | 99 | — | — |
| 5 | U5 snrna | rna | 141 | — | — |
| A | Pre-mRNA-splicing factor 8 | protein | 1914 | 46% helix, 10% strand | P33334 |
| C | Pre-mRNA-splicing factor SNU114 | protein | 874 | 35% helix, 18% strand | P36048 |
| H | Pre-mRNA-splicing factor CWC22 | protein | 401 | 73% helix, 0% strand | P53333 |
| J | Pre-mRNA-splicing factor PRP46 | protein | 342 | 3% helix, 40% strand | Q12417 |
| K | Pre-mRNA-processing protein 45 | protein | 187 | 39% helix, 3% strand | P28004 |
| L | Pre-mRNA-splicing factor BUD31 | protein | 155 | 52% helix, 0% strand | P25337 |
| M | Pre-mRNA-splicing factor CWC2 | protein | 252 | 30% helix, 13% strand | Q12046 |
| N | Pre-mRNA-splicing factor SLT11 | protein | 227 | 38% helix, 15% strand | P38241 |
| O | Pre-mRNA-splicing factor CEF1 | protein | 211 | 62% helix, 0% strand | Q03654 |
| P | Pre-mRNA-splicing factor CWC15 | protein | 69 | 20% helix, 0% strand | Q03772 |
| R | Pre-mRNA-splicing factor CWC21 | protein | 108 | 66% helix, 3% strand | Q03375 |
| S | Pre-mRNA-splicing factor CLF1 | protein | 468 | 82% helix, 0% strand | Q12309 |
| T | Pre-mRNA-splicing factor SYF1 | protein | 338 | 78% helix, 0% strand | Q04048 |
| a | Pre-mRNA-splicing factor 18 | protein | 137 | 71% helix, 0% strand | P33411 |
| c | Pre-mRNA-splicing factor SLU7 | protein | 103 | 60% helix, 0% strand | Q02775 |
| o | Pre-mRNA-processing factor 17 | protein | 313 | 4% helix, 30% strand | P40968 |
| X | Unknown | protein | 68 | 81% helix, 0% strand | — |
| y | Pre-mRNA-splicing factor SYF2 | protein | 83 | 65% helix, 7% strand | P53277 |
| b | Small nuclear ribonucleoprotein-associated protein B | protein | 80 | 4% helix, 49% strand | P40018 |
| d | Small nuclear ribonucleoprotein sm D3 | protein | 82 | 13% helix, 38% strand | P43321 |
| e | Small nuclear ribonucleoprotein E | protein | 75 | 19% helix, 32% strand | Q12330 |
| f | Small nuclear ribonucleoprotein F | protein | 72 | 10% helix, 47% strand | P54999 |
| g | Small nuclear ribonucleoprotein G | protein | 69 | 0% helix, 45% strand | P40204 |
| h | Small nuclear ribonucleoprotein sm D1 | protein | 82 | 15% helix, 44% strand | Q02260 |
| j | Small nuclear ribonucleoprotein sm D2 | protein | 94 | 23% helix, 43% strand | Q06217 |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · chains A, c
- GTP · Guanosine-5'-triphosphate · ligand · chains A, C
- ZN · Zinc ion · metal · 6 copies · chains L, 6, M, N
- MG · Magnesium ion · metal · 3 copies · chains E, 6, A
- K · Potassium ion · metal · 2 copies · chains 6
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 | 1056 | 0.89 | 0.90 | 112 | GTP |
| 2 | 961 | 0.89 | 0.90 | 120 | empty |
| 3 | 924 | 0.87 | 0.88 | 92 | empty |
| 4 | 717 | 0.86 | 0.90 | 68 | empty |
| 5 | 759 | 0.84 | 0.88 | 54 | empty |
Interfaces
105 interfaces between chains.
- A–C · 4591 Ų buried · 39 hydrogen bonds · protein-protein
- 5–A · 3883 Ų buried · 86 hydrogen bonds · protein-nucleic
- A–K · 2555 Ų buried · 17 hydrogen bonds · protein-protein
- O–S · 2205 Ų buried · 30 hydrogen bonds · protein-protein
- A–c · 2185 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5MPS · Structure of a spliceosome remodeled for exon ligation · the same entry in another collection · chain h against h, 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 P53333
- 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 Q03772
- Every structure of UniProt Q03375
- Every structure of UniProt Q12309
- Every structure of UniProt Q04048
- Every structure of UniProt P33411
- Every structure of UniProt Q02775
- Every structure of UniProt P40968
- Every structure of UniProt P53277
- 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 5MPS · PDBe 5MPS · UniProt P33334 · UniProt P36048 · UniProt P53333 · UniProt Q12417 · UniProt P28004 · UniProt P25337 · UniProt Q12046 · UniProt P38241 · UniProt Q03654 · UniProt Q03772 · UniProt Q03375 · UniProt Q12309 · UniProt Q04048 · UniProt P33411 · UniProt Q02775 · UniProt P40968 · UniProt P53277 · UniProt P40018 · UniProt P43321 · UniProt Q12330 · UniProt P54999 · UniProt P40204 · UniProt Q02260 · UniProt Q06217
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