Research workbench
Vanadate at the active site of a small ribozyme suggests a role for water in transition-state stabilization
Analyse Vanadate at the active site of a small ribozyme suggests a role for water in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2P7E
- Type
- RNA
- Length
- 61 nucleotides
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5' substrate strand, pentameric fragment; Ribozyme strand I; Ribozyme strand II; Ribozyme…
- Ligands
- NCO, S9L, SO4
- Pockets
- 3 · best druggability 0.42
Structure
x-ray diffraction · 5 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5' substrate strand, pentameric fragment | rna | 5 | — | — |
| B | Ribozyme strand I | rna | 12 | — | — |
| C | Ribozyme strand II | rna | 17 | — | — |
| D | Ribozyme strand III | rna | 19 | — | — |
| P | 3' substrate strand, octameric fragment | rna | 8 | — | — |
Ligands and binding sites
- NCO · Cobalt hexammine(iii) · ligand · 2 copies · chains A, B, C, D
- S9L · 2-[2-(2-hydroxyethoxy)ethoxy]ethyl dihydrogen phosphate · ligand · chains B, C, D
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 199 | 0.42 | 0.73 | 15 | empty |
| 2 | 169 | 0.40 | 0.73 | 19 | empty |
| 3 | 168 | 0.40 | 0.73 | 17 | empty |
Interfaces
9 interfaces between chains.
- C–D · 894 Ų buried · 73 hydrogen bonds · nucleic-nucleic
- B–P · 391 Ų buried · 28 hydrogen bonds · nucleic-nucleic
- A–B · 298 Ų buried · 26 hydrogen bonds · nucleic-nucleic
- B–C · 207 Ų buried · 7 hydrogen bonds · nucleic-nucleic
- A–D · 195 Ų buried · 4 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 covalent, 1 modified (covalent ligand, nucleotide modification).
Compared structures
- 2P7E · Vanadate at the Active Site of a Small Ribozyme Suggests a Role for Water in… · the same entry in another collection · chain D against D, 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
- Elsewhere: RCSB PDB 2P7E · PDBe 2P7E
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