Research workbench
Pbp acca from a. tumefaciens C58
Analyse Pbp acca from a. tumefaciens C58 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZE8
- Type
- protein
- Length
- 1,964 residues
- Chains
- 4
- 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
- SO4
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | ABC transporter, substrate binding protein (agrocinopines a and B) | protein | 491 | 31% helix, 23% strand | Q7D2F4 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, D
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.72 | 0.88 | 36 | EDO |
| 2 | 233 | 0.71 | 0.87 | 36 | EDO |
| 3 | 394 | 0.71 | 0.82 | 54 | empty |
| 4 | 221 | 0.70 | 0.87 | 36 | PEG, EDO |
| 5 | 228 | 0.70 | 0.86 | 38 | GOL |
Interfaces
5 interfaces between chains.
- B–D · 851 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 409 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 356 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 269 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 72 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4ZE8 · PBP AccA from A. tumefaciens C58 · 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 4ZE8 · PDBe 4ZE8 · UniProt Q7D2F4
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