Research workbench
Triosephosphate isomerase of vibrio marinus complexed with 2-phosphoglycolate
Analyse Triosephosphate isomerase of vibrio marinus complexed with 2-phosphoglycolate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1AW1
- Type
- protein
- Length
- 2,036 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Triosephosphate isomerase
- EC
- 5.3.1.1
- UniProt
- P50921
- Ligands
- PGA
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | Triosephosphate isomerase (EC 5.3.1.1) | protein | 255 | 50% helix, 15% strand | P50921 |
| B, E, H, K | Triosephosphate isomerase (EC 5.3.1.1) | protein | 254 | 50% helix, 16% strand | P50921 |
Ligands and binding sites
- PGA · 2-phosphoglycolic acid · ligand · 8 copies · chains A, B, D, E, G, H, J, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.71 | 0.90 | 43 | empty |
| 2 | 146 | 0.71 | 0.90 | 38 | empty |
| 3 | 162 | 0.71 | 0.90 | 40 | empty |
| 4 | 157 | 0.68 | 0.88 | 41 | empty |
| 5 | 264 | 0.60 | 0.79 | 39 | empty |
Interfaces
11 interfaces between chains.
- J–K · 1728 Ų buried · 36 hydrogen bonds · protein-protein
- G–H · 1727 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 1724 Ų buried · 36 hydrogen bonds · protein-protein
- D–E · 1719 Ų buried · 36 hydrogen bonds · protein-protein
- D–J · 365 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1AW1 · Triosephosphate isomerase of vibrio marinus complexed with 2-phosphoglycolate · the same entry in another collection · chain E against E, TM-score 1.00
- P50921 · AlphaFold monomer V2.0 prediction for triosephosphate isomerase (P50921) · a predicted model of the same protein · 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 P50921
- Elsewhere: RCSB PDB 1AW1 · PDBe 1AW1 · UniProt P50921
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