Research workbench
Crystal structure of the class I ligase ribozyme-substrate preligation complex, C47U mutant, CA2+ bound
Analyse Crystal structure of the class I ligase ribozyme-substrate preligation complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R1H
- Type
- protein + RNA
- Length
- 459 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- U1 small nuclear ribonucleoprotein a; 5'-R(*UP*CP*CP*AP*GP*UP*A)-3'; Class I ligase…
- UniProt
- P09012
- Ligands
- CA
- Pockets
- 13 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | U1 small nuclear ribonucleoprotein a | protein | 92 | 30% helix, 23% strand | P09012 |
| B, E | 5'-R(*UP*CP*CP*AP*GP*UP*A)-3' | rna | 7 | — | — |
| C, F | Class I ligase ribozyme | rna | 130 | — | — |
| D | U1 small nuclear ribonucleoprotein a | protein | 93 | 32% helix, 19% strand | P09012 |
Ligands and binding sites
- CA · Calcium ion · metal · 26 copies · chains C, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 568 | 0.71 | 0.81 | 29 | CA |
| 2 | 445 | 0.67 | 0.80 | 34 | empty |
| 3 | 451 | 0.67 | 0.80 | 34 | empty |
| 4 | 386 | 0.67 | 0.81 | 21 | CA |
| 5 | 344 | 0.65 | 0.81 | 30 | CA |
Interfaces
5 interfaces between chains.
- A–C · 959 Ų buried · 30 hydrogen bonds · protein-nucleic
- D–F · 936 Ų buried · 33 hydrogen bonds · protein-nucleic
- B–C · 690 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- E–F · 656 Ų buried · 29 hydrogen bonds · nucleic-nucleic
- A–D · 164 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 3R1H · Crystal structure of the Class I ligase ribozyme-substrate preligation complex, C47U… · the same entry in another collection · chain A against A, 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 3R1H · PDBe 3R1H · UniProt P09012
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