MolNFT v1 · #69491 · protein
Crystal structure of putative glycerophosphoryl diester phosphodiesterase (17743486) from agrobacterium tumefaciens str. C58 (dupont) at 2.05 a resolution
3KS5: “Crystal structure of putative glycerophosphoryl diester phosphodiesterase (17743486) from agrobacterium…”. X-ray diffraction, 1 ligand (FE). MolNFT v1 #69491 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3KS5
- Type
- protein
- Length
- 495 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerophosphoryl diester phosphodiesterase
- UniProt
- A9CLR1
- Ligands
- FE
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycerophosphoryl diester phosphodiesterase | protein | 247 | 43% helix, 21% strand | A9CLR1 |
| B | Glycerophosphoryl diester phosphodiesterase | protein | 248 | 42% helix, 21% strand | A9CLR1 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B
- ACT · Acetate ion · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 3KS5 · Crystal structure of Putative glycerophosphoryl diester phosphodiesterase (17743486) from… · 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 A9CLR1
- Elsewhere: RCSB PDB 3KS5 · PDBe 3KS5 · UniProt A9CLR1
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