MolNFT v1 · #105546 · protein
NAD(P)H:QUINONE oxidoreductase from methanothermobacter marburgensis
4R81 · NADH dehydrogenase: “NAD(P)H:QUINONE oxidoreductase from methanothermobacter marburgensis”. X-ray diffraction, 1 ligand (FMN), 5 pockets (best druggability 0.77). MolNFT v1 #105546 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4R81
- Type
- protein
- Length
- 794 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH dehydrogenase
- UniProt
- D9PVS9
- Ligands
- FMN
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | NADH dehydrogenase | protein | 199 | 40% helix, 18% strand | D9PVS9 |
| B | NADH dehydrogenase | protein | 199 | 41% helix, 19% strand | D9PVS9 |
| C | NADH dehydrogenase | protein | 197 | 41% helix, 21% strand | D9PVS9 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.77 | 0.91 | 29 | empty |
| 2 | 467 | 0.76 | 0.85 | 39 | FMN |
| 3 | 458 | 0.75 | 0.83 | 42 | FMN |
| 4 | 471 | 0.73 | 0.82 | 43 | FMN |
| 5 | 447 | 0.71 | 0.81 | 40 | FMN |
Interfaces
3 interfaces between chains.
- A–B · 1660 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1620 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1059 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4R81 · NAD(P)H:qui oxidoreductase from Methanothermobacter marburgensis · 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 D9PVS9
- Elsewhere: RCSB PDB 4R81 · PDBe 4R81 · UniProt D9PVS9
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