Research workbench
Transition state stabilization by a catalytic RNA
Analyse Transition state stabilization by a catalytic RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1M5P
- Type
- protein + RNA
- Length
- 410 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA inhibitor substrate; RNA hairpin ribozyme; U1 small nuclear ribonucleoprotein a
- UniProt
- P09012
- Ligands
- CA
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | RNA inhibitor substrate | rna | 12 | — | — |
| M, P | RNA inhibitor substrate | rna | 9 | — | — |
| B, E | RNA hairpin ribozyme | rna | 92 | — | — |
| C, F | U1 small nuclear ribonucleoprotein a | protein | 92 | 29% helix, 27% strand | P09012 |
Ligands and binding sites
- CA · Calcium ion · metal · 26 copies · chains B, A, P, E, F, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1110 | 0.69 | 0.75 | 48 | CA |
| 2 | 888 | 0.68 | 0.75 | 46 | CA |
| 3 | 832 | 0.67 | 0.75 | 57 | CA |
| 4 | 580 | 0.65 | 0.77 | 30 | empty |
| 5 | 441 | 0.55 | 0.74 | 25 | CA |
Interfaces
9 interfaces between chains.
- E–F · 959 Ų buried · 32 hydrogen bonds · protein-nucleic
- B–C · 958 Ų buried · 33 hydrogen bonds · protein-nucleic
- D–E · 875 Ų buried · 59 hydrogen bonds · nucleic-nucleic
- A–B · 793 Ų buried · 62 hydrogen bonds · nucleic-nucleic
- P–E · 664 Ų buried · 48 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 1M5P · Transition State Stabilization by a Catalytic RNA · 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 1M5P · PDBe 1M5P · UniProt P09012
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