MolNFT v1 · #191190 · protein
Crystal structure of the lactate dehydrogenase of cyanobacterium aponinum in complex with oxamate, NADH and fbp.
8AB3 · L-lactate dehydrogenase: “Crystal structure of the lactate dehydrogenase of cyanobacterium aponinum in complex with oxamate, NADH and…”. X-ray diffraction, 3 ligands (OXM, NAI, FBP), 20 pockets (best druggability 0.82). MolNFT v1…
- PDB
- 8AB3
- Type
- protein
- Length
- 1,316 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lactate dehydrogenase
- EC
- 1.1.1.27
- UniProt
- K9Z684
- Ligands
- OXM, NAI, FBP
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 330 | 46% helix, 19% strand | K9Z684 |
| B, D | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 328 | 47% helix, 19% strand | K9Z684 |
Ligands and binding sites
- OXM · Oxamic acid · ligand · 4 copies · chains A, B, C, D
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- FBP · 1,6-di-O-phosphono-beta-D-fructofuranose · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 485 | 0.82 | 0.89 | 52 | FBP |
| 2 | 425 | 0.82 | 0.90 | 46 | FBP |
| 3 | 237 | 0.70 | 0.86 | 37 | OXM, NAI |
| 4 | 280 | 0.69 | 0.84 | 42 | OXM, NAI |
| 5 | 250 | 0.69 | 0.84 | 37 | OXM, NAI |
Interfaces
6 interfaces between chains.
- B–C · 2711 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 2702 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1999 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 1939 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1031 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 8AB3 · Crystal Structure of the Lactate Dehydrogenase of Cyanobacterium Aponinum in complex with… · 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 K9Z684
- Elsewhere: RCSB PDB 8AB3 · PDBe 8AB3 · UniProt K9Z684
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