Research workbench
Ni-mediated dimer of maltose-binding protein A216H/K220H by synthetic symmetrization (form II)
Analyse Ni-mediated dimer 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
- 3SEX
- Type
- protein
- Length
- 740 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltose-binding periplasmic protein
- UniProt
- P0AEX9
- Ligands
- GLC, NI, IOD
- Pockets
- 7 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Maltose-binding periplasmic protein | protein | 370 | 45% helix, 21% strand | P0AEX9 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, C
- NI · Nickel (II) ion · metal · 2 copies · chains A, C
- IOD · Iodide ion · ion · 26 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1026 | 0.88 | 0.90 | 92 | GLC, IOD |
| 2 | 350 | 0.69 | 0.82 | 42 | IOD |
| 3 | 138 | 0.62 | 0.86 | 28 | IOD |
| 4 | 71 | 0.41 | 0.79 | 16 | IOD |
| 5 | 64 | 0.38 | 0.79 | 14 | IOD |
Interfaces
1 interface between chains.
- A–C · 815 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3SEX · Ni-mediated Dimer 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 3SEX · PDBe 3SEX · UniProt P0AEX9
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