Research workbench
Twinning in crystals of human skeletal muscle D-glyceraldehyde-3- phosphate dehydrogenase
Analyse Twinning in crystals of human skeletal muscle 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
- 3GPD
- Type
- protein
- Length
- 668 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
- P00354
- Ligands
- NAD, SO4
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R, G | D-glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 334 | 29% helix, 22% strand | P00354 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains R, G
- SO4 · Sulfate ion · ion · 4 copies · chains R, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 805 | 0.71 | 0.77 | 72 | SO4, NAD |
| 2 | 765 | 0.71 | 0.77 | 66 | SO4, NAD |
| 3 | 54 | 0.45 | 0.84 | 19 | empty |
| 4 | 56 | 0.27 | 0.74 | 14 | empty |
| 5 | 50 | 0.27 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- R–G · 1218 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 isopeptide (isopeptide).
Compared structures
- 3GPD · Twinning in crystals of human skeletal muscle D-glyceraldehyde-3-phosphate dehydrogenase · the same entry in another collection · chain R against R, 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 P00354
- Elsewhere: RCSB PDB 3GPD · PDBe 3GPD · UniProt P00354
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