MolNFT v1 · #142659 · protein
The apo-structure of D-lactate dehydrogenase from fusobacterium nucleatum
6ABI: “The apo-structure of D-lactate dehydrogenase from fusobacterium nucleatum”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.71). MolNFT v1 #142659 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ABI
- Type
- protein
- Length
- 664 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-lactate dehydrogenase
- EC
- 1.1.1.28
- UniProt
- Q8RG11
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-lactate dehydrogenase (EC 1.1.1.28) | protein | 333 | 38% helix, 18% strand | Q8RG11 |
| B | D-lactate dehydrogenase (EC 1.1.1.28) | protein | 331 | 37% helix, 19% strand | Q8RG11 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 686 | 0.71 | 0.78 | 80 | SO4 |
| 2 | 355 | 0.63 | 0.79 | 42 | SO4, GOL |
| 3 | 136 | 0.51 | 0.80 | 27 | GOL |
| 4 | 116 | 0.40 | 0.76 | 19 | GOL |
| 5 | 52 | 0.23 | 0.71 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 3066 Ų buried · 56 hydrogen bonds · protein-protein
Compared structures
- 6ABI · The apo-structure of D-lactate dehydrogenase from Fusobacterium nucleatum · 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 Q8RG11
- Elsewhere: RCSB PDB 6ABI · PDBe 6ABI · UniProt Q8RG11
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