MolNFT v1 · #83973 · protein
On archaeal homologs of the human RNase P proteins POP5 and RPP30 in the hyperthermophilic archaeon thermococcus kodakarensis
3WZ0 · Ribonuclease P protein component 3: “On archaeal homologs of the human RNase P proteins POP5 and RPP30 in the hyperthermophilic archaeon…”. X-ray diffraction, 4 pockets (best druggability 0.30). MolNFT v1 #83973 on GenesisL1: 3D…
- PDB
- 3WZ0
- Type
- protein
- Length
- 621 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease P protein component 3; Ribonuclease P protein component 2
- EC
- 3.1.26.5
- UniProt
- Q5JH47, Q5JJ62
- Pockets
- 4 · best druggability 0.30
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, F | Ribonuclease P protein component 3 (EC 3.1.26.5) | protein | 206 | 51% helix, 19% strand | Q5JH47 |
| C | Ribonuclease P protein component 2 (EC 3.1.26.5) | protein | 105 | 42% helix, 34% strand | Q5JJ62 |
| A | Ribonuclease P protein component 2 (EC 3.1.26.5) | protein | 104 | 42% helix, 31% strand | Q5JJ62 |
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 89 | 0.30 | 0.72 | 18 | empty |
| 2 | 60 | 0.27 | 0.73 | 15 | empty |
| 3 | 58 | 0.25 | 0.72 | 12 | empty |
| 4 | 50 | 0.25 | 0.73 | 13 | empty |
Interfaces
5 interfaces between chains.
- E–C · 838 Ų buried · 8 hydrogen bonds · protein-protein
- F–A · 824 Ų buried · 9 hydrogen bonds · protein-protein
- C–A · 493 Ų buried · 9 hydrogen bonds · protein-protein
- E–A · 480 Ų buried · 1 hydrogen bond · protein-protein
- F–C · 472 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3WZ0 · On archaeal homologs of the human RNase P proteins Pop5 and Rpp30 in the… · the same entry in another collection · chain E against E, TM-score 1.00
- Q5JH47 · AlphaFold monomer V2.0 prediction for ribonuclease P protein component 3 (Q5JH47) · a predicted model of the same protein · chain E against A, TM-score 0.99
- Q5JJ62 · AlphaFold monomer V2.0 prediction for ribonuclease P protein component 2 (Q5JJ62) · a predicted model of the same protein · chain C 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 Q5JH47
- Every structure of UniProt Q5JJ62
- Elsewhere: RCSB PDB 3WZ0 · PDBe 3WZ0 · UniProt Q5JH47 · UniProt Q5JJ62
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