Research workbench
Crystal structure of glycerophosphodiester phosphodiesterase from agrobacterium tumefaciens STR.C58
Analyse Crystal structure of glycerophosphodiester phosphodiesterase from agrobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZCC
- Type
- protein
- Length
- 1,400 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerophosphodiester phosphodiesterase
- UniProt
- Q8U887
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycerophosphodiester phosphodiesterase | protein | 240 | 39% helix, 20% strand | Q8U887 |
| B | Glycerophosphodiester phosphodiesterase | protein | 228 | 37% helix, 21% strand | Q8U887 |
| C | Glycerophosphodiester phosphodiesterase | protein | 233 | 39% helix, 21% strand | Q8U887 |
| D | Glycerophosphodiester phosphodiesterase | protein | 231 | 37% helix, 22% strand | Q8U887 |
| E | Glycerophosphodiester phosphodiesterase | protein | 233 | 37% helix, 21% strand | Q8U887 |
| F | Glycerophosphodiester phosphodiesterase | protein | 235 | 39% helix, 20% strand | Q8U887 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D, E, F
- ACT · Acetate ion · additive · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1125 | 0.83 | 0.84 | 142 | empty |
| 2 | 400 | 0.74 | 0.84 | 59 | empty |
| 3 | 330 | 0.73 | 0.86 | 63 | empty |
| 4 | 391 | 0.71 | 0.83 | 54 | empty |
| 5 | 209 | 0.66 | 0.85 | 34 | empty |
Interfaces
12 interfaces between chains.
- D–E · 745 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 745 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 739 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 733 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 719 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1ZCC · Crystal structure of glycerophosphodiester phosphodiesterase from Agrobacterium… · 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 Q8U887
- Elsewhere: RCSB PDB 1ZCC · PDBe 1ZCC · UniProt Q8U887
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