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Crystallographic structure of glyceraldehyde-3-phosphate dehydrogenase from schistosoma mansoni
Analyse Crystallographic structure of glyceraldehyde-3-phosphate dehydrogenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JH0
- Type
- protein
- Length
- 1,352 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase
- EC
- 1.2.1.12
- UniProt
- P20287
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 338 | 29% helix, 26% strand | P20287 |
| D | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 338 | 28% helix, 26% strand | P20287 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, D, B
- PGE · Triethylene glycol · additive · 2 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B, D
- EDO · 1,2-ethanediol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 421 | 0.73 | 0.83 | 62 | empty |
| 2 | 928 | 0.72 | 0.76 | 122 | empty |
| 3 | 809 | 0.71 | 0.77 | 112 | GOL, PEG |
| 4 | 56 | 0.70 | 0.97 | 23 | empty |
| 5 | 433 | 0.70 | 0.81 | 58 | EDO |
Interfaces
6 interfaces between chains.
- B–C · 2040 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 2018 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1444 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1441 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 505 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard, oxidation).
Compared structures
- 7JH0 · Crystallographic structure of glyceraldehyde-3-phosphate dehydrogenase from Schistosoma… · the same entry in another collection · chain D against D, TM-score 1.00
- P20287 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase (P20287) · 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 P20287
- Elsewhere: RCSB PDB 7JH0 · PDBe 7JH0 · UniProt P20287
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