MolNFT v1 · #185826 · protein
Cryo-EM structure of ldh-etfab complex from acetobacterium woodii
7QH2 · Lactate dehydrogenase (NAD(+),FERREDOXIN) subunit lctc: “Cryo-EM structure of ldh-etfab complex from acetobacterium woodii”. Electron microscopy, 2 ligands (FAD, FE), 20 pockets (best druggability 0.87). MolNFT v1 #185826 on…
- PDB
- 7QH2
- Type
- protein
- Length
- 2,138 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactate dehydrogenase (NAD(+),FERREDOXIN) subunit lctc; Lactate dehydrogenase…
- EC
- 1.3.1.110
- UniProt
- H6LBB1, H6LBB0, H6LBS1
- Ligands
- FAD, FE
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Lactate dehydrogenase (NAD(+),FERREDOXIN) subunit lctc (EC 1.3.1.110) | protein | 337 | 29% helix, 26% strand | H6LBB1 |
| B, E | Lactate dehydrogenase (NAD(+),FERREDOXIN) subunit lctb (EC 1.3.1.110) | protein | 265 | 26% helix, 26% strand | H6LBB0 |
| C, F | Lactate dehydrogenase (NAD(+),FERREDOXIN) subunit lctd (EC 1.3.1.110) | protein | 467 | 39% helix, 20% strand | H6LBS1 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 6 copies · chains A, C, B, D, F, E
- FE · Fe (III) ion · metal · 2 copies · chains C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1053 | 0.87 | 0.89 | 108 | empty |
| 2 | 781 | 0.85 | 0.88 | 80 | FAD |
| 3 | 741 | 0.84 | 0.88 | 78 | FAD |
| 4 | 578 | 0.73 | 0.81 | 57 | FAD |
| 5 | 595 | 0.73 | 0.80 | 63 | FAD |
Interfaces
7 interfaces between chains.
- D–E · 3617 Ų buried · 51 hydrogen bonds · protein-protein
- A–B · 3596 Ų buried · 44 hydrogen bonds · protein-protein
- C–F · 3187 Ų buried · 31 hydrogen bonds · protein-protein
- E–F · 852 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 828 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7QH2 · Cryo-EM structure of Ldh-EtfAB complex from Acetobacterium woodii · 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 H6LBB1
- Every structure of UniProt H6LBB0
- Every structure of UniProt H6LBS1
- Elsewhere: RCSB PDB 7QH2 · PDBe 7QH2 · UniProt H6LBB1 · UniProt H6LBB0 · UniProt H6LBS1
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