Research workbench
The crystal structure of D-lactate dehydrogenase from escherichia COLI
Analyse The crystal structure of D-lactate dehydrogenase from escherichia COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WX0
- Type
- protein
- Length
- 1,128 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
- EC
- 1.1.1.28
- UniProt
- C6EEW4
- Pockets
- 18 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding (EC 1.1.1.28) | protein | 303 | 42% helix, 18% strand | C6EEW4 |
| B | D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding (EC 1.1.1.28) | protein | 274 | 36% helix, 18% strand | C6EEW4 |
| C | D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding (EC 1.1.1.28) | protein | 264 | 44% helix, 14% strand | C6EEW4 |
| D | D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding (EC 1.1.1.28) | protein | 287 | 40% helix, 18% strand | C6EEW4 |
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.61 | 0.84 | 32 | empty |
| 2 | 223 | 0.60 | 0.80 | 28 | empty |
| 3 | 142 | 0.60 | 0.84 | 27 | empty |
| 4 | 147 | 0.60 | 0.83 | 28 | empty |
| 5 | 452 | 0.59 | 0.75 | 49 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2607 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 2437 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 564 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 433 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 393 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3WX0 · The crystal structure of D-lactate dehydrogenase from Escherichia coli · 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 C6EEW4
- Elsewhere: RCSB PDB 3WX0 · PDBe 3WX0 · UniProt C6EEW4
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