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Crystal structure of the domain comprising the NAD binding and the FAD binding regions of the NADH:UBIQUINONE oxidoreductase, na translocating, F subunit from porphyromonas gingivalis
Analyse Crystal structure of the domain comprising the NAD binding and the FAD binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R6H
- Type
- protein
- Length
- 1,144 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH:UBIQUINONE oxidoreductase, na translocating, F subunit
- EC
- 1.6.5.-
- UniProt
- Q7MT22
- Ligands
- FAD, SO4
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NADH:UBIQUINONE oxidoreductase, na translocating, F subunit (EC 1.6.5.-) | protein | 285 | 28% helix, 31% strand | Q7MT22 |
| B | NADH:UBIQUINONE oxidoreductase, na translocating, F subunit (EC 1.6.5.-) | protein | 286 | 30% helix, 30% strand | Q7MT22 |
| C | NADH:UBIQUINONE oxidoreductase, na translocating, F subunit (EC 1.6.5.-) | protein | 289 | 30% helix, 31% strand | Q7MT22 |
| D | NADH:UBIQUINONE oxidoreductase, na translocating, F subunit (EC 1.6.5.-) | protein | 284 | 29% helix, 31% strand | Q7MT22 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 11 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1006 | 0.81 | 0.82 | 105 | empty |
| 2 | 979 | 0.79 | 0.80 | 95 | SO4 |
| 3 | 642 | 0.67 | 0.76 | 64 | FAD |
| 4 | 426 | 0.63 | 0.77 | 53 | FAD |
| 5 | 278 | 0.55 | 0.77 | 31 | empty |
Interfaces
5 interfaces between chains.
- C–D · 802 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 778 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 750 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 675 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 123 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 modified (engineered).
Compared structures
- 2R6H · Crystal structure of the domain comprising the NAD binding and the FAD binding regions of… · 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 Q7MT22
- Elsewhere: RCSB PDB 2R6H · PDBe 2R6H · UniProt Q7MT22
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