Research workbench
Pbp acca from a. tumefaciens C58 in complex with agrocinopine-3'-O- benzoate
Analyse Pbp acca from a. tumefaciens C58 in complex with agrocinopine-3'-O- benzoate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZED
- Type
- protein
- Length
- 490 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
- AGW
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 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 |
Ligands and binding sites
- AGW · [(2S,3S,4R,5R)-2,5-bis(hydroxymethyl)-2-[(2R,3R,4R,5R,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4-[oxidanyl-[(2R,3R,4S,5S)-2,4,5-tris(oxidanyl)oxan-3-yl]oxy-phosphoryl]oxy-oxolan-3-yl] benzoate · ligand · chains A
- EDO · 1,2-ethanediol · additive · 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 | 253 | 0.74 | 0.88 | 36 | empty |
| 2 | 578 | 0.72 | 0.80 | 54 | AGW |
| 3 | 121 | 0.47 | 0.79 | 25 | empty |
| 4 | 51 | 0.28 | 0.75 | 18 | empty |
Compared structures
- 4ZED · PBP AccA from A. tumefaciens C58 in complex with agrocinopine-3'-O-benzoate · 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 4ZED · PDBe 4ZED · UniProt Q7D2F4
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