Research workbench
The apo-structure of D-lactate dehydrogenase from escherichia COLI
Analyse The apo-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
- 5Z1Z
- Type
- protein
- Length
- 1,256 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
- UniProt
- A0A140N893
- Ligands
- MG
- Pockets
- 14 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding | protein | 315 | 41% helix, 18% strand | A0A140N893 |
| B | D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding | protein | 314 | 40% helix, 18% strand | A0A140N893 |
| C | D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding | protein | 316 | 40% helix, 18% strand | A0A140N893 |
| D | D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding | protein | 311 | 37% helix, 19% strand | A0A140N893 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 829 | 0.72 | 0.77 | 102 | empty |
| 2 | 571 | 0.66 | 0.76 | 66 | empty |
| 3 | 335 | 0.63 | 0.79 | 50 | empty |
| 4 | 295 | 0.61 | 0.79 | 32 | empty |
| 5 | 297 | 0.60 | 0.78 | 42 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2757 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 2610 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 618 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 591 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 367 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5Z1Z · The apo-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 A0A140N893
- Elsewhere: RCSB PDB 5Z1Z · PDBe 5Z1Z · UniProt A0A140N893
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