Research workbench
Crystal structure of ndh with NADH
Analyse Crystal structure of ndh with NADH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4G6H
- Type
- protein
- Length
- 944 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial
- EC
- 1.6.5.9
- UniProt
- P32340
- Ligands
- FAD, NAI, MG
- Pockets
- 16 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial (EC 1.6.5.9) | protein | 472 | 37% helix, 26% strand | P32340 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 286 | 0.80 | 0.91 | 35 | empty |
| 2 | 305 | 0.79 | 0.90 | 36 | empty |
| 3 | 692 | 0.79 | 0.83 | 66 | NAI, FAD |
| 4 | 1012 | 0.78 | 0.80 | 87 | FAD, NAI |
| 5 | 102 | 0.76 | 0.97 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 2126 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
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 P32340
- Elsewhere: RCSB PDB 4G6H · PDBe 4G6H · UniProt P32340
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