Research workbench
Crystal structure of triosephosphate isomerase from schistosoma mansoni in complex with 2PG
Analyse Crystal structure of triosephosphate isomerase from schistosoma mansoni in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OOI
- Type
- protein
- Length
- 2,003 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Triosephosphate isomerase
- EC
- 5.3.1.1
- UniProt
- P48501
- Ligands
- PGA, NA, CL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | Triosephosphate isomerase (EC 5.3.1.1) | protein | 250 | 43% helix, 17% strand | P48501 |
| B, E, G | Triosephosphate isomerase (EC 5.3.1.1) | protein | 249 | 44% helix, 17% strand | P48501 |
| C | Triosephosphate isomerase (EC 5.3.1.1) | protein | 255 | 42% helix, 16% strand | P48501 |
| D | Triosephosphate isomerase (EC 5.3.1.1) | protein | 251 | 44% helix, 17% strand | P48501 |
| F | Triosephosphate isomerase (EC 5.3.1.1) | protein | 250 | 44% helix, 17% strand | P48501 |
Ligands and binding sites
- PGA · 2-phosphoglycolic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- NA · Sodium ion · metal · 8 copies · chains A, B, C, E, H
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D, F, G
- GOL · Glycerol · additive · 2 copies · chains C, D, H, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 964 | 0.86 | 0.88 | 136 | empty |
| 2 | 744 | 0.74 | 0.79 | 72 | CL |
| 3 | 72 | 0.74 | 0.98 | 25 | empty |
| 4 | 72 | 0.73 | 0.98 | 26 | empty |
| 5 | 66 | 0.73 | 0.98 | 23 | empty |
Interfaces
16 interfaces between chains.
- E–F · 1629 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1621 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1618 Ų buried · 31 hydrogen bonds · protein-protein
- G–H · 1608 Ų buried · 29 hydrogen bonds · protein-protein
- B–F · 468 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6OOI · Crystal structure of triosephosphate isomerase from Schistosoma mansoni in complex with… · the same entry in another collection · chain H against H, TM-score 1.00
- P48501 · AlphaFold monomer V2.0 prediction for triosephosphate isomerase (P48501) · a predicted model of the same protein · chain B 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 P48501
- Elsewhere: RCSB PDB 6OOI · PDBe 6OOI · UniProt P48501
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