Research workbench
Babesia orientalis lactate dehydrogenase, boldh apo
Analyse Babesia orientalis lactate dehydrogenase, boldh apo in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7W8A
- Type
- protein
- Length
- 2,375 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactate dehydrogenase
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 8 distinct chains · 48% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactate dehydrogenase | protein | 311 | 49% helix, 21% strand | — |
| B | Lactate dehydrogenase | protein | 294 | 49% helix, 21% strand | — |
| C | Lactate dehydrogenase | protein | 301 | 48% helix, 21% strand | — |
| D | Lactate dehydrogenase | protein | 292 | 49% helix, 22% strand | — |
| E | Lactate dehydrogenase | protein | 293 | 49% helix, 22% strand | — |
| F | Lactate dehydrogenase | protein | 292 | 47% helix, 22% strand | — |
| G | Lactate dehydrogenase | protein | 292 | 48% helix, 22% strand | — |
| H | Lactate dehydrogenase | protein | 300 | 48% helix, 21% strand | — |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1008 | 0.86 | 0.87 | 103 | empty |
| 2 | 1140 | 0.86 | 0.87 | 103 | empty |
| 3 | 70 | 0.74 | 0.98 | 23 | empty |
| 4 | 71 | 0.73 | 0.98 | 19 | empty |
| 5 | 67 | 0.72 | 0.98 | 20 | empty |
Interfaces
15 interfaces between chains.
- E–H · 2284 Ų buried · 19 hydrogen bonds · protein-protein
- F–G · 2243 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 2224 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 2196 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1499 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 7W8A · Babesia orientalis lactate dehydrogenase, BoLDH apo · 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
- Elsewhere: RCSB PDB 7W8A · PDBe 7W8A
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