Research workbench
Crystal structure of pyrococcus furiosus POP5, an archaeal ribonuclease P protein
Analyse Crystal structure of pyrococcus furiosus POP5, an archaeal ribonuclease P… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AV5
- Type
- protein
- Length
- 530 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease P protein component 2
- EC
- 3.1.26.5
- UniProt
- Q8U151
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Ribonuclease P protein component 2 (EC 3.1.26.5) | protein | 106 | 42% helix, 34% strand | Q8U151 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 684 | 0.67 | 0.76 | 68 | empty |
| 2 | 199 | 0.49 | 0.75 | 23 | empty |
| 3 | 103 | 0.48 | 0.80 | 16 | empty |
| 4 | 71 | 0.34 | 0.76 | 19 | empty |
Interfaces
5 interfaces between chains.
- C–E · 550 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 360 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 350 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 342 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 193 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2AV5 · Crystal structure of Pyrococcus furiosus Pop5, an archaeal Ribonuclease P protein · the same entry in another collection · chain B against B, TM-score 1.00
- Q8U151 · AlphaFold monomer V2.0 prediction for ribonuclease P protein component 2 (Q8U151) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q8U151
- Elsewhere: RCSB PDB 2AV5 · PDBe 2AV5 · UniProt Q8U151
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