Research workbench
Zn-mediated polymer of maltose-binding protein A216H/K220H by synthetic symmetrization (form II)
Analyse Zn-mediated polymer of maltose-binding protein A216H/K220H by synthetic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SEY
- Type
- protein
- Length
- 1,112 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltose-binding periplasmic protein
- UniProt
- P0AEX9
- Ligands
- GLC, ZN
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Maltose-binding periplasmic protein | protein | 371 | 46% helix, 20% strand | P0AEX9 |
| E | Maltose-binding periplasmic protein | protein | 370 | 45% helix, 21% strand | P0AEX9 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 6 copies · chains A, C, E
- ZN · Zinc ion · metal · 23 copies · chains A, C, E
- ACT · Acetate ion · additive · 8 copies · chains A, C, E
- GOL · Glycerol · additive · 5 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1135 | 0.77 | 0.79 | 90 | GLC, ZN, ACT, GOL |
| 2 | 334 | 0.70 | 0.83 | 32 | GLC |
| 3 | 317 | 0.69 | 0.83 | 37 | GLC |
| 4 | 329 | 0.59 | 0.77 | 51 | empty |
| 5 | 132 | 0.46 | 0.77 | 21 | empty |
Interfaces
2 interfaces between chains.
- A–C · 441 Ų buried · 6 hydrogen bonds · protein-protein
- C–E · 402 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3SEY · Zn-mediated Polymer of Maltose-binding Protein A216H/K220H by Synthetic Symmetrization… · the same entry in another collection · chain A against A, TM-score 1.00
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
- Elsewhere: RCSB PDB 3SEY · PDBe 3SEY · UniProt P0AEX9
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