Research workbench
Crystal structure of glyceraldehyde-3-phosphate dehydrogenase gapn from methanocaldococcus jannaschii dsm 2661
Analyse Crystal structure of glyceraldehyde-3-phosphate dehydrogenase gapn from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PQA
- Type
- protein
- Length
- 1,825 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactaldehyde dehydrogenase
- EC
- 1.2.1.22
- UniProt
- Q58806
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactaldehyde dehydrogenase (EC 1.2.1.22) | protein | 456 | 45% helix, 23% strand | Q58806 |
| B | Lactaldehyde dehydrogenase (EC 1.2.1.22) | protein | 458 | 44% helix, 22% strand | Q58806 |
| C | Lactaldehyde dehydrogenase (EC 1.2.1.22) | protein | 455 | 44% helix, 23% strand | Q58806 |
| D | Lactaldehyde dehydrogenase (EC 1.2.1.22) | protein | 456 | 44% helix, 23% strand | Q58806 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 289 | 0.82 | 0.93 | 51 | empty |
| 2 | 235 | 0.79 | 0.93 | 31 | empty |
| 3 | 215 | 0.79 | 0.93 | 38 | empty |
| 4 | 178 | 0.78 | 0.94 | 38 | empty |
| 5 | 289 | 0.78 | 0.90 | 40 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2353 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 2319 Ų buried · 38 hydrogen bonds · protein-protein
- A–D · 1068 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1057 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 822 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3PQA · Crystal structure of glyceraldehyde-3-phosphate dehydrogenase GapN from… · the same entry in another collection · chain D against D, TM-score 1.00
- Q58806 · AlphaFold monomer V2.0 prediction for lactaldehyde dehydrogenase (Q58806) · a predicted model of the same protein · chain A against A, 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 Q58806
- Elsewhere: RCSB PDB 3PQA · PDBe 3PQA · UniProt Q58806
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