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Crystal structure of D-isomer specific 2-hydroxyacid dehydrogenase from lactobacillus delbrueckii ssp. bulgaricus
Analyse Crystal structure of D-isomer specific 2-hydroxyacid dehydrogenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YQ4
- Type
- protein
- Length
- 1,308 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-isomer specific 2-hydroxyacid dehydrogenase
- UniProt
- Q1GAA2
- Pockets
- 14 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-isomer specific 2-hydroxyacid dehydrogenase | protein | 328 | 40% helix, 17% strand | Q1GAA2 |
| B | D-isomer specific 2-hydroxyacid dehydrogenase | protein | 328 | 39% helix, 17% strand | Q1GAA2 |
| C | D-isomer specific 2-hydroxyacid dehydrogenase | protein | 331 | 41% helix, 16% strand | Q1GAA2 |
| D | D-isomer specific 2-hydroxyacid dehydrogenase | protein | 321 | 40% helix, 16% strand | Q1GAA2 |
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 716 | 0.72 | 0.78 | 76 | empty |
| 2 | 785 | 0.71 | 0.77 | 56 | empty |
| 3 | 707 | 0.70 | 0.77 | 56 | empty |
| 4 | 683 | 0.68 | 0.76 | 61 | empty |
| 5 | 334 | 0.68 | 0.82 | 44 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2838 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 2792 Ų buried · 38 hydrogen bonds · protein-protein
- A–D · 626 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 599 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 239 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2YQ4 · Crystal Structure of D-isomer specific 2-hydroxyacid dehydrogenase from Lactobacillus… · the same entry in another collection · chain D against D, 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 Q1GAA2
- Elsewhere: RCSB PDB 2YQ4 · PDBe 2YQ4 · UniProt Q1GAA2
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