Research workbench
The crystal structure of holo-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic bacterium thermotoga maritima at 2.5 ångströms resolution
Analyse The crystal structure of holo-glyceraldehyde-3-phosphate dehydrogenase from the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HDG
- Type
- protein
- Length
- 664 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Holo-D-glyceraldehyde-3-phosphate dehydrogenase
- EC
- 1.2.1.12
- UniProt
- P17721
- Ligands
- NAD, SO4
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O, Q | Holo-D-glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 332 | 31% helix, 27% strand | P17721 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains O, Q
- SO4 · Sulfate ion · ion · 4 copies · chains O, Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 740 | 0.72 | 0.78 | 76 | SO4, NAD |
| 2 | 480 | 0.68 | 0.79 | 46 | SO4, NAD |
| 3 | 138 | 0.46 | 0.77 | 16 | empty |
| 4 | 100 | 0.43 | 0.78 | 14 | empty |
| 5 | 74 | 0.31 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- O–Q · 571 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1HDG · The crystal structure of holo-glyceraldehyde-3-phosphate dehydrogenase from the… · the same entry in another collection · chain O against O, TM-score 1.00
- P17721 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase (P17721) · a predicted model of the same protein · chain Q 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 P17721
- Elsewhere: RCSB PDB 1HDG · PDBe 1HDG · UniProt P17721
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