Research workbench
Crystal structure of the lactate dehydrogenase of cyanobacterium aponinum in complex with oxamate, NADH and fbp.
Analyse Crystal structure of the lactate dehydrogenase of cyanobacterium aponinum in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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