MolNFT v2 · #142129 · protein
Structure of the Brx1 and Ebp2 complex
5Z1G · rRNA-processing protein EBP2: “Structure of the Brx1 and Ebp2 complex”. X-ray diffraction at 2.294, 1 ligand (SO4), 9 pockets (best druggability 0.75). MolNFT v2 #142129 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5Z1G
- Type
- protein
- Length
- 622 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.294
- Source
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
- Molecule
- rRNA-processing protein EBP2; Ribosome biogenesis protein BRX1
- UniProt
- P36049, Q08235
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · resolution 2.294 · 2 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | rRNA-processing protein EBP2 | protein | 99 | 49% helix, 4% strand | P36049 |
| B, D | Ribosome biogenesis protein BRX1 | protein | 212 | 23% helix, 36% strand | Q08235 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 638 | 0.75 | 0.81 | 50 | empty |
| 2 | 126 | 0.42 | 0.76 | 18 | empty |
| 3 | 69 | 0.39 | 0.79 | 20 | empty |
| 4 | 113 | 0.38 | 0.75 | 21 | empty |
| 5 | 101 | 0.37 | 0.75 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–D · 3034 Ų buried · 51 hydrogen bonds · protein-protein
- B–C · 3029 Ų buried · 50 hydrogen bonds · protein-protein
- A–C · 223 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 156 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 138 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5Z1G · Structure of the BRX1 and EBP2 complex · the same entry in another collection · chain D against D, TM-score 1.00
- Q08235 · AlphaFold monomer V2.0 prediction for ribosome biogenesis protein BRX1 (Q08235) · a predicted model of the same protein · chain D against A, TM-score 0.99
- P36049 · AlphaFold monomer V2.0 prediction for rRNA-processing protein EBP2 (P36049) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 P36049
- Every structure of UniProt Q08235
- Elsewhere: RCSB PDB 5Z1G · PDBe 5Z1G · UniProt P36049 · UniProt Q08235
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.