MolNFT v1 · #80978 · protein + RNA
The C92U mutant C-di-gmp-I riboswitch bound to gpa
3UD4 · U1 small nuclear ribonucleoprotein a: “The C92U mutant C-di-gmp-I riboswitch bound to gpa”. X-ray diffraction, 1 ligand (MG), 3 pockets (best druggability 0.70). MolNFT v1 #80978 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3UD4
- Type
- protein + RNA
- Length
- 181 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- U1 small nuclear ribonucleoprotein a; RNA (92-mer); RNA (5'-R(*GP*A)-3')
- UniProt
- P09012
- Ligands
- MG
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | U1 small nuclear ribonucleoprotein a | protein | 87 | 30% helix, 26% strand | P09012 |
| R | RNA (92-mer) | rna | 92 | — | — |
| B | RNA (5'-R(*GP*A)-3') | rna | 2 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 655 | 0.70 | 0.79 | 42 | empty |
| 2 | 561 | 0.67 | 0.78 | 32 | empty |
| 3 | 434 | 0.60 | 0.77 | 30 | empty |
Interfaces
2 interfaces between chains.
- P–R · 1059 Ų buried · 28 hydrogen bonds · protein-nucleic
- R–B · 486 Ų buried · 23 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3UD4 · The C92U mutant c-di-GMP-I riboswitch bound to GpA · 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 P09012
- Elsewhere: RCSB PDB 3UD4 · PDBe 3UD4 · UniProt P09012
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