Research workbench
Crystal structure of hydroxypyruvic acid phosphate bound D-3- phosphoglycerate dehydrogenase in mycobacterium tuberculosis
Analyse Crystal structure of hydroxypyruvic acid phosphate bound D-3- phosphoglycerate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DDN
- Type
- protein
- Length
- 1,052 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-3-phosphoglycerate dehydrogenase
- EC
- 1.1.1.95
- UniProt
- P0A544
- Ligands
- HPV
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95) | protein | 527 | 33% helix, 25% strand | P0A544 |
| B | D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95) | protein | 525 | 34% helix, 26% strand | P0A544 |
Ligands and binding sites
- HPV · 2-oxo-3-(phosphonooxy)propanoic acid · ligand · chains A, B
- TLA · L(+)-tartaric acid · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 873 | 0.81 | 0.84 | 63 | empty |
| 2 | 1048 | 0.77 | 0.79 | 104 | HPV |
| 3 | 298 | 0.53 | 0.75 | 47 | empty |
| 4 | 79 | 0.48 | 0.82 | 18 | empty |
| 5 | 70 | 0.47 | 0.83 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2610 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 3DDN · Crystal structure of hydroxypyruvic acid phosphate bound D-3-phosphoglycerate… · the same entry in another collection · 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 P0A544
- Elsewhere: RCSB PDB 3DDN · PDBe 3DDN · UniProt P0A544
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