Research workbench
Schiff base intermediate in kdpg aldolase from escherichia COLI
Analyse Schiff base intermediate in kdpg aldolase from escherichia COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EUA
- Type
- protein
- Length
- 639 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kdpg aldolase
- EC
- 4.1.2.14
- UniProt
- P0A955
- Ligands
- PYR, SO4
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Kdpg aldolase (EC 4.1.2.14) | protein | 213 | 44% helix, 17% strand | P0A955 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 222 | 0.75 | 0.90 | 27 | ACT |
| 2 | 95 | 0.69 | 0.92 | 23 | empty |
| 3 | 173 | 0.50 | 0.77 | 31 | SO4 |
| 4 | 111 | 0.41 | 0.76 | 28 | SO4 |
| 5 | 97 | 0.37 | 0.75 | 20 | SO4 |
Interfaces
3 interfaces between chains.
- B–C · 616 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 598 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 584 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
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 P0A955
- Elsewhere: RCSB PDB 1EUA · PDBe 1EUA · UniProt P0A955
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