Research workbench
Structure of active-site carboxymethylated D-glyceraldehyde-3- phosphate dehydrogenase from palinurus versicolor
Analyse Structure of active-site carboxymethylated D-glyceraldehyde-3- phosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DSS
- Type
- protein
- Length
- 666 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-glyceraldehyde-3-phosphate-dehydrogenase
- EC
- 1.2.1.12
- UniProt
- P56649
- Ligands
- NAD, SO4
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, R | D-glyceraldehyde-3-phosphate-dehydrogenase (EC 1.2.1.12) | protein | 333 | 32% helix, 26% strand | P56649 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains G, R
- SO4 · Sulfate ion · ion · 4 copies · chains G, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 567 | 0.67 | 0.77 | 65 | SO4, NAD |
| 2 | 542 | 0.66 | 0.77 | 64 | SO4, NAD |
Interfaces
1 interface between chains.
- G–R · 1372 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 1DSS · Structure of active-site carboxymethylated D-glyceraldehyde-3-phosphate dehydrogenase… · the same entry in another collection · chain G against G, TM-score 1.00
- P56649 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase (P56649) · a predicted model of the same protein · chain G 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 P56649
- Elsewhere: RCSB PDB 1DSS · PDBe 1DSS · UniProt P56649
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.