Research workbench
Se-pbp acca from a. tumefaciens C58 in complex with agrocinopine a
Analyse Se-pbp acca from a. tumefaciens C58 in complex with agrocinopine a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZE9
- Type
- protein
- Length
- 489 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ABC transporter, substrate binding protein (agrocinopines a and B)
- UniProt
- Q7D2F4
- Ligands
- TT7, 4GL, ARA
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ABC transporter, substrate binding protein (agrocinopines a and B) | protein | 489 | 32% helix, 22% strand | Q7D2F4 |
Ligands and binding sites
- TT7 · 4-O-phosphono-beta-D-fructofuranose · ligand · chains A
- 4GL · alpha-D-gulopyranose · ligand · chains A
- ARA · alpha-L-arabinopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 539 | 0.74 | 0.82 | 55 | TT7, 4GL, ARA |
| 2 | 242 | 0.72 | 0.87 | 38 | empty |
| 3 | 104 | 0.46 | 0.80 | 20 | empty |
| 4 | 53 | 0.27 | 0.74 | 15 | empty |
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 4ZE9 · Se-PBP AccA from A. tumefaciens C58 in complex with agrocinopine A · 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 Q7D2F4
- Elsewhere: RCSB PDB 4ZE9 · PDBe 4ZE9 · UniProt Q7D2F4
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