Research workbench
A relaxed active site following exon ligation by a group I intron
Analyse A relaxed active site following exon ligation by a group I intron in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BO4
- Type
- protein + RNA
- Length
- 317 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Group I intron P9; DNA/RNA (5'- R(*AP*AP*GP*CP*CP*AP*CP*AP*CP*AP*AP*AP*CP*CP*A)-D(P*DG)-3'…
- UniProt
- P09012
- Ligands
- MG, K
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Group I intron P9 | rna | 197 | — | — |
| C | DNA/RNA (5'- R(*AP*AP*GP*CP*CP*AP*CP*AP*CP*AP*AP*AP*CP*CP*A)-D(P*DG)-3') | rna | 16 | — | — |
| D | DNA/RNA (5'-R(*CP*A)-D(P*DU)-R(P*AP*CP*GP*GP*CP*C)-3') | rna | 9 | — | — |
| A | U1 small nuclear ribonucleoprotein a | protein | 95 | 22% helix, 25% strand | P09012 |
Ligands and binding sites
- MG · Magnesium ion · metal · 12 copies · chains B, D, C
- K · Potassium ion · metal · 6 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 531 | 0.76 | 0.85 | 51 | K, MG |
| 2 | 916 | 0.73 | 0.78 | 38 | empty |
| 3 | 197 | 0.57 | 0.82 | 21 | MG |
| 4 | 474 | 0.57 | 0.74 | 32 | K |
| 5 | 212 | 0.54 | 0.79 | 18 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1380 Ų buried · 80 hydrogen bonds · nucleic-nucleic
- B–A · 1026 Ų buried · 24 hydrogen bonds · protein-nucleic
- B–D · 803 Ų buried · 55 hydrogen bonds · nucleic-nucleic
- C–D · 35 Ų buried · 0 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3BO4 · A relaxed active site following exon ligation by a group I intron · the same entry in another collection · chain B against B, 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 3BO4 · PDBe 3BO4 · UniProt P09012
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