Research workbench
Pbp acca from a. tumefaciens C58 in complex with L-arabinose-2- isopropylphosphate
Analyse Pbp acca from a. tumefaciens C58 in complex with L-arabinose-2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZEK
- 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)
- Ligands
- LAH, TOE
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ABC transporter, substrate binding protein (agrocinopines a and B) | protein | 490 | 31% helix, 24% strand | — |
Ligands and binding sites
- LAH · 2-O-[(R)-hydroxy(propan-2-yloxy)phosphoryl]-alpha-L-arabinopyranose · ligand · chains A
- TOE · 2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxyl · ligand · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 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 | 0.73 | 0.81 | 54 | LAH |
| 2 | 244 | 0.72 | 0.87 | 39 | empty |
| 3 | 110 | 0.48 | 0.80 | 20 | empty |
Compared structures
- 4ZEK · PBP AccA from A. tumefaciens C58 in complex with L-arabinose-2-isopropylphosphate · 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
- Elsewhere: RCSB PDB 4ZEK · PDBe 4ZEK
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