Research workbench
Crystal structure of PML B-box2
Analyse Crystal structure of PML B-box2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8J2P
- Type
- protein
- Length
- 826 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.09
- Source
- Escherichia coli (strain K12); Homo sapiens
- Molecule
- Maltose/maltodextrin-binding periplasmic protein,Protein PML
- EC
- 2.3.2.-
- UniProt
- P0AEX9, P29590
- Ligands
- GLC, ZN
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · resolution 2.09 · 1 distinct chain · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, A | Maltose/maltodextrin-binding periplasmic protein,Protein PML (EC 2.3.2.-) | protein | 413 | 42% helix, 21% strand | P0AEX9, P29590 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains E, A
- ZN · Zinc ion · metal · 4 copies · chains E, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 802 | 0.78 | 0.82 | 86 | GLC |
| 2 | 406 | 0.71 | 0.82 | 39 | GLC |
| 3 | 193 | 0.53 | 0.78 | 36 | empty |
| 4 | 87 | 0.52 | 0.84 | 18 | empty |
| 5 | 63 | 0.48 | 0.85 | 18 | empty |
Interfaces
1 interface between chains.
- E–A · 597 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- P0AEX9 · AlphaFold monomer V2.0 prediction for MALTOSE/MALTODEXTRIN-binding periplasmic protein… · a predicted model of the same protein · chain A against A, TM-score 0.89
- P29590 · AlphaFold monomer V2.0 prediction for protein pml (P29590) · a predicted model of the same protein · chain E against A, TM-score 0.28
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 P0AEX9
- Every structure of UniProt P29590
- Elsewhere: RCSB PDB 8J2P · PDBe 8J2P · UniProt P0AEX9 · UniProt P29590
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