Research workbench
Crystallographic analysis of the complex between triosephosphate isomerase and 2-phosphoglycolate at 2.5- ångströms resolution. implications for catalysis
Analyse Crystallographic analysis of the complex between triosephosphate isomerase and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YPI
- Type
- protein
- Length
- 494 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Triosephosphate isomerase
- EC
- 5.3.1.1
- UniProt
- P00942
- Ligands
- PGA
- Pockets
- 2 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Triosephosphate isomerase (EC 5.3.1.1) | protein | 247 | 40% helix, 14% strand | P00942 |
Ligands and binding sites
- PGA · 2-phosphoglycolic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 94 | 0.58 | 0.86 | 22 | empty |
| 2 | 64 | 0.41 | 0.81 | 24 | PGA |
Interfaces
1 interface between chains.
- A–B · 1670 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 2YPI · Crystallographic analysis of the complex between triosephosphate isomerase and… · the same entry in another collection · chain A against A, TM-score 1.00
- P00942 · AlphaFold monomer V2.0 prediction for triosephosphate isomerase (P00942) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P00942
- Elsewhere: RCSB PDB 2YPI · PDBe 2YPI · UniProt P00942
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