Research workbench
Crystal structure of archeal RNase P protein PH1481P in complex with PH1877P
Analyse Crystal structure of archeal RNase P protein PH1481P in complex with PH1877P in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CZV
- Type
- protein
- Length
- 651 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
- O59543, O59150
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease P protein component 3 (EC 3.1.26.5) | protein | 208 | 49% helix, 17% strand | O59543 |
| B | Ribonuclease P protein component 3 (EC 3.1.26.5) | protein | 206 | 50% helix, 17% strand | O59543 |
| C | Ribonuclease P protein component 2 (EC 3.1.26.5) | protein | 118 | 41% helix, 29% strand | O59150 |
| D | Ribonuclease P protein component 2 (EC 3.1.26.5) | protein | 119 | 39% helix, 30% strand | O59150 |
Ligands and binding sites
- ACY · Acetic acid · additive · 16 copies · chains A, C, B, D
- BOG · octyl beta-D-glucopyranoside · additive · 2 copies · chains A, C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 535 | 0.69 | 0.78 | 48 | BOG |
| 2 | 321 | 0.57 | 0.76 | 35 | empty |
| 3 | 155 | 0.44 | 0.75 | 27 | ACY |
| 4 | 78 | 0.40 | 0.79 | 16 | ACY |
| 5 | 61 | 0.39 | 0.80 | 14 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1038 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1020 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 963 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 946 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 385 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 2CZV · Crystal structure of archeal RNase P protein ph1481p in complex with ph1877p · the same entry in another collection · chain D against D, TM-score 1.00
- O59150 · AlphaFold monomer V2.0 prediction for ribonuclease P protein component 2 (O59150) · a predicted model of the same protein · chain C against A, TM-score 1.00
- O59543 · AlphaFold monomer V2.0 prediction for ribonuclease P protein component 3 (O59543) · a predicted model of the same protein · chain B 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 O59543
- Every structure of UniProt O59150
- Elsewhere: RCSB PDB 2CZV · PDBe 2CZV · UniProt O59543 · UniProt O59150
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