Research workbench
Crystal structure of two D-glyceraldehyde-3-phosphate dehydrogenase complexes: a case of asymmetry
Analyse Crystal structure of two D-glyceraldehyde-3-phosphate dehydrogenase complexes… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IHX
- Type
- protein
- Length
- 1,332 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
- P56649
- Ligands
- SND, SO4
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glyceraldehyde 3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 333 | 32% helix, 25% strand | P56649 |
Ligands and binding sites
- SND · Thionicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1005 | 0.83 | 0.84 | 121 | empty |
| 2 | 1139 | 0.73 | 0.76 | 124 | SO4, SND |
| 3 | 582 | 0.66 | 0.77 | 63 | SO4, SND |
| 4 | 496 | 0.64 | 0.77 | 58 | SO4, SND |
| 5 | 61 | 0.30 | 0.75 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2034 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 2009 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1350 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 1344 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 527 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1IHX · Crystal structure of two D-glyceraldehyde-3-phosphate dehydrogenase complexes: a case of… · the same entry in another collection · chain C against C, TM-score 1.00
- P56649 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase (P56649) · a predicted model of the same protein · chain D 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 1IHX · PDBe 1IHX · UniProt P56649
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