MolNFT v1 · #14329 · protein + RNA
Transition state stabilization by a catalytic RNA
1M5V · RNA inhibitor substrate: “Transition state stabilization by a catalytic RNA”. X-ray diffraction, 1 ligand (CA), 9 pockets (best druggability 0.69). MolNFT v1 #14329 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1M5V
- Type
- protein + RNA
- Length
- 414 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
- 9 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 26% 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 | 94 | 32% helix, 26% strand | P09012 |
Ligands and binding sites
- CA · Calcium ion · metal · 34 copies · chains B, C, A, D, E, P
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1072 | 0.69 | 0.75 | 47 | CA |
| 2 | 901 | 0.68 | 0.75 | 46 | CA |
| 3 | 610 | 0.66 | 0.77 | 30 | CA |
| 4 | 696 | 0.64 | 0.75 | 39 | CA |
| 5 | 460 | 0.55 | 0.74 | 25 | empty |
Interfaces
9 interfaces between chains.
- E–F · 951 Ų buried · 32 hydrogen bonds · protein-nucleic
- B–C · 924 Ų buried · 32 hydrogen bonds · protein-nucleic
- D–E · 896 Ų buried · 56 hydrogen bonds · nucleic-nucleic
- A–B · 798 Ų buried · 54 hydrogen bonds · nucleic-nucleic
- M–B · 651 Ų buried · 49 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 1M5V · 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 1M5V · PDBe 1M5V · UniProt P09012
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