Research workbench
Pbp acca from a. tumefaciens C58 in complex with agrocin 84
Analyse Pbp acca from a. tumefaciens C58 in complex with agrocin 84 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZEC
- 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
- Q52012
- Ligands
- C84
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ABC transporter, substrate binding protein (agrocinopines a and B) | protein | 490 | 33% helix, 25% strand | Q52012 |
Ligands and binding sites
- C84 · [(2R,3R,4S,5S,6R)-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl]oxy-N-[9-[(2R,3S,5R)-5-[[[(2R,3S)-4-methyl-2,3-bis(oxidanyl)pentanoyl]amino]-oxidanyl-phosphoryl]oxy-3-oxidanyl-oxolan-2-yl]purin-6-yl]phosphonamidic acid · ligand · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
- GOL · Glycerol · 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 | 243 | 0.73 | 0.87 | 37 | empty |
| 2 | 529 | 0.72 | 0.81 | 48 | C84 |
| 3 | 131 | 0.47 | 0.78 | 26 | EDO |
| 4 | 57 | 0.37 | 0.80 | 17 | PEG |
Compared structures
- 4ZEC · PBP AccA from A. tumefaciens C58 in complex with agrocin 84 · 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 Q52012
- Elsewhere: RCSB PDB 4ZEC · PDBe 4ZEC · UniProt Q52012
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