MolNFT v1 · #75270 · protein + RNA
Crystal structure of a catalytically active substrate-bound box C/D rnp from sulfolobus solfataricus
3PLA · Pre mRNA splicing protein: “Crystal structure of a catalytically active substrate-bound box C/D rnp from sulfolobus solfataricus”. X-ray diffraction, 1 ligand (SAH), 18 pockets (best druggability 0.85). MolNFT v1 #75270 on…
- PDB
- 3PLA
- Type
- protein + RNA
- Length
- 2,300 residues
- Chains
- 15
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pre mRNA splicing protein; 50S ribosomal protein L7AE; Fibrillarin-like RRNA/TRNA…
- EC
- 2.1.1.-
- UniProt
- Q97ZH3, D0KRE2, P58032
- Ligands
- SAH
- Pockets
- 18 · best druggability 0.85
Structure
x-ray diffraction · 7 distinct chains · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, K | Pre mRNA splicing protein | protein | 375 | 65% helix, 7% strand | Q97ZH3 |
| C, D, L | 50S ribosomal protein L7AE | protein | 122 | 47% helix, 16% strand | D0KRE2 |
| E, F, M | Fibrillarin-like RRNA/TRNA 2'-O-methyltransferase (EC 2.1.1.-) | protein | 227 | 27% helix, 33% strand | P58032 |
| G | C/D guide RNA | rna | 35 | — | — |
| H | C/D guide RNA | rna | 32 | — | — |
| I, J, O | RNA (5'-R(*CP*CP*AP*UP*GP*AP*GP*UP*GP*U)-3') | rna | 10 | — | — |
| N | C/D guide RNA | rna | 31 | — | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 3 copies · chains E, G, I, F, H, J, M, N, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1044 | 0.85 | 0.86 | 84 | empty |
| 2 | 1074 | 0.84 | 0.86 | 89 | empty |
| 3 | 167 | 0.81 | 0.97 | 29 | SAH |
| 4 | 171 | 0.81 | 0.96 | 33 | SAH |
| 5 | 1054 | 0.81 | 0.82 | 100 | empty |
Interfaces
40 interfaces between chains.
- A–B · 1804 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 1489 Ų buried · 15 hydrogen bonds · protein-protein
- B–F · 1489 Ų buried · 15 hydrogen bonds · protein-protein
- K–M · 1473 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 1315 Ų buried · 95 hydrogen bonds · nucleic-nucleic
Compared structures
- 3PLA · Crystal structure of a catalytically active substrate-bound box C/D RNP from Sulfolobus… · the same entry in another collection · chain O against O, 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 Q97ZH3
- Every structure of UniProt D0KRE2
- Every structure of UniProt P58032
- Elsewhere: RCSB PDB 3PLA · PDBe 3PLA · UniProt Q97ZH3 · UniProt D0KRE2 · UniProt P58032
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