MolNFT v1 · #172702 · protein + RNA
Human pre-bact-2 spliceosome core structure
7AAV · 116 kda U5 small nuclear ribonucleoprotein component: “Human pre-bact-2 spliceosome core structure”. Electron microscopy, 3 ligands (GTP, KGN, MG), 20 pockets (best druggability 0.89). MolNFT v1 #172702 on GenesisL1: 3D structure…
- PDB
- 7AAV
- Type
- protein + RNA
- Length
- 4,151 residues
- Chains
- 17
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 116 kda U5 small nuclear ribonucleoprotein component; Protein BUD31 homolog; Cell…
- UniProt
- Q15029, P41223, Q99459, Q9P013, P55081, O43660, O60508, Q8NAV1, Q6P2Q9, Q9NW64, Q13573, Q96NC0, Q9BZL1
- Ligands
- GTP, KGN, MG
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 17 distinct chains · 33% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| r | 116 kda U5 small nuclear ribonucleoprotein component | protein | 895 | 27% helix, 14% strand | Q15029 |
| Q | Protein BUD31 homolog | protein | 138 | 38% helix, 0% strand | P41223 |
| L | Cell division cycle 5-like protein | protein | 103 | 60% helix, 0% strand | Q99459 |
| R | Spliceosome-associated protein CWC15 homolog | protein | 44 | 14% helix, 2% strand | Q9P013 |
| K | Microfibrillar-associated protein 1 | protein | 123 | 34% helix, 0% strand | P55081 |
| G | Pleiotropic regulator 1 | protein | 320 | 0% helix, 38% strand | O43660 |
| Z | Minx M3 pre-mRNA | rna | 29 | — | — |
| 8 | Pre-mRNA-processing factor 17 | protein | 18 | 50% helix, 6% strand | O60508 |
| I | Pre-mRNA-splicing factor 38A | protein | 176 | 47% helix, 9% strand | Q8NAV1 |
| A | Pre-mRNA-processing-splicing factor 8 | protein | 1656 | 42% helix, 7% strand | Q6P2Q9 |
| P | Pre-mRNA-splicing factor RBM22 | protein | 162 | 20% helix, 14% strand | Q9NW64 |
| v | Snw domain-containing protein 1 | protein | 206 | 35% helix, 4% strand | Q13573 |
| N | Zinc finger matrin-type protein 2 | protein | 56 | 38% helix, 0% strand | Q96NC0 |
| 2 | U2 snrna | rna | 10 | — | — |
| 5 | U5 snrna | rna | 69 | — | — |
| 6 | U6 snrna | rna | 73 | — | — |
| q | Ubiquitin-like protein 5 | protein | 73 | 21% helix, 33% strand | Q9BZL1 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains r
- KGN · D-chiro inositol hexakisphosphate · ligand · chains K, Z, A
- MG · Magnesium ion · metal · chains r
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 | 1052 | 0.89 | 0.91 | 166 | empty |
| 2 | 985 | 0.88 | 0.89 | 122 | empty |
| 3 | 715 | 0.86 | 0.90 | 100 | empty |
| 4 | 657 | 0.84 | 0.89 | 92 | empty |
| 5 | 984 | 0.84 | 0.85 | 83 | empty |
Interfaces
47 interfaces between chains.
- r–A · 2807 Ų buried · 11 hydrogen bonds · protein-protein
- A–5 · 1902 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–v · 1827 Ų buried · 7 hydrogen bonds · protein-protein
- K–A · 1068 Ų buried · 6 hydrogen bonds · protein-protein
- A–q · 1049 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7AAV · Human pre-Bact-2 spliceosome core structure · the same entry in another collection · chain P against P, 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 Q15029
- Every structure of UniProt P41223
- Every structure of UniProt Q99459
- Every structure of UniProt Q9P013
- Every structure of UniProt P55081
- Every structure of UniProt O43660
- Every structure of UniProt O60508
- Every structure of UniProt Q8NAV1
- Every structure of UniProt Q6P2Q9
- Every structure of UniProt Q9NW64
- Every structure of UniProt Q13573
- Every structure of UniProt Q96NC0
- Every structure of UniProt Q9BZL1
- Elsewhere: RCSB PDB 7AAV · PDBe 7AAV · UniProt Q15029 · UniProt P41223 · UniProt Q99459 · UniProt Q9P013 · UniProt P55081 · UniProt O43660 · UniProt O60508 · UniProt Q8NAV1 · UniProt Q6P2Q9 · UniProt Q9NW64 · UniProt Q13573 · UniProt Q96NC0 · UniProt Q9BZL1
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