Research workbench
Structure of tagatose-1,6-bisphosphate aldolase
Analyse Structure of tagatose-1,6-bisphosphate aldolase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GVF
- Type
- protein
- Length
- 548 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tagatose-bisphosphate aldolase agay
- EC
- 4.1.2.40
- UniProt
- P42908
- Ligands
- PGH, ZN, NA
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tagatose-bisphosphate aldolase agay (EC 4.1.2.40) | protein | 273 | 51% helix, 15% strand | P42908 |
| B | Tagatose-bisphosphate aldolase agay (EC 4.1.2.40) | protein | 275 | 52% helix, 14% strand | P42908 |
Ligands and binding sites
- PGH · Phosphoglycolohydroxamic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 455 | 0.66 | 0.79 | 70 | EDO |
| 2 | 274 | 0.63 | 0.81 | 42 | EDO |
| 3 | 54 | 0.41 | 0.82 | 19 | PGH |
| 4 | 53 | 0.36 | 0.80 | 18 | PGH |
Interfaces
1 interface between chains.
- A–B · 654 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1GVF · Structure of tagatose-1,6-bisphosphate aldolase · 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 P42908
- Elsewhere: RCSB PDB 1GVF · PDBe 1GVF · UniProt P42908
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