Research workbench
Pbp acca from a. tumefaciens C58 in complex with agrocinopine a
Analyse 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
- 4ZEB
- Type
- protein
- Length
- 979 residues
- Chains
- 2
- 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
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ABC transporter, substrate binding protein (agrocinopines a and B) | protein | 490 | 33% helix, 23% strand | Q7D2F4 |
| B | ABC transporter, substrate binding protein (agrocinopines a and B) | protein | 489 | 33% helix, 23% strand | Q7D2F4 |
Ligands and binding sites
- TT7 · 4-O-phosphono-beta-D-fructofuranose · ligand · 2 copies · chains A, B
- 4GL · alpha-D-gulopyranose · ligand · 2 copies · chains A, B
- ARA · alpha-L-arabinopyranose · sugar · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 527 | 0.74 | 0.82 | 49 | TT7, 4GL, ARA |
| 2 | 508 | 0.74 | 0.82 | 47 | TT7, 4GL, ARA |
| 3 | 237 | 0.72 | 0.87 | 37 | empty |
| 4 | 219 | 0.72 | 0.88 | 37 | empty |
| 5 | 89 | 0.45 | 0.80 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 13 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4ZEB · 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 4ZEB · PDBe 4ZEB · UniProt Q7D2F4
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