Research workbench
Crystal structure of a NAD-dependent D-glycerate dehydrogenase at 2.4 ångströms resolution
Analyse Crystal structure of a NAD-dependent D-glycerate dehydrogenase at 2.4 ångströms… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GDH
- Type
- protein
- Length
- 640 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-glycerate dehydrogenase
- EC
- 1.1.1.29
- UniProt
- P36234
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | D-glycerate dehydrogenase (EC 1.1.1.29) | protein | 320 | 37% helix, 18% strand | P36234 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 486 | 0.64 | 0.76 | 42 | empty |
| 2 | 477 | 0.63 | 0.77 | 47 | empty |
| 3 | 167 | 0.49 | 0.77 | 28 | empty |
| 4 | 54 | 0.25 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 3247 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 1GDH · Crystal structure of a NAD-dependent D-glycerate dehydrogenase at 2.4 ångströms resolution · the same entry in another collection · chain A against A, TM-score 1.00
- P36234 · AlphaFold monomer V2.0 prediction for glycerate dehydrogenase (P36234) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P36234
- Elsewhere: RCSB PDB 1GDH · PDBe 1GDH · UniProt P36234
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