MolNFT v1 · #154132 · protein
Crystal structure basis for bmldh complex
6K13 · L-lactate dehydrogenase: “Crystal structure basis for bmldh complex”. X-ray diffraction, 2 ligands (OXM, NAD), 9 pockets (best druggability 0.72). MolNFT v1 #154132 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6K13
- Type
- protein
- Length
- 655 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lactate dehydrogenase
- EC
- 1.1.1.27
- UniProt
- I7J7V6
- Ligands
- OXM, NAD
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 332 | 47% helix, 18% strand | I7J7V6 |
| B | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 323 | 47% helix, 18% strand | I7J7V6 |
Ligands and binding sites
- OXM · Oxamic acid · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 227 | 0.72 | 0.88 | 39 | OXM, NAD |
| 2 | 224 | 0.69 | 0.86 | 41 | OXM, NAD |
| 3 | 135 | 0.55 | 0.82 | 24 | empty |
| 4 | 204 | 0.47 | 0.74 | 29 | empty |
| 5 | 185 | 0.46 | 0.74 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 2834 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6K13 · Crystal Structure Basis for BmLDH Complex · 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 I7J7V6
- Elsewhere: RCSB PDB 6K13 · PDBe 6K13 · UniProt I7J7V6
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