MolNFT v1 · #173161 · protein
Cryo-EM structure of arabidopsis thaliana complex-I (peripheral arm)
7AQR · NADH dehydrogenase [ubiquinone] iron-sulfur protein 7…: “Cryo-EM structure of arabidopsis thaliana complex-I (peripheral arm)”. Electron microscopy, 6 ligands (SF4, FES, FMN), 20 pockets (best druggability 0.82). MolNFT v1 #173161…
- PDB
- 7AQR
- Type
- protein
- Length
- 3,249 residues
- Chains
- 17
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial; NADH dehydrogenase…
- EC
- 7.1.1.2
- UniProt
- Q42577, Q95748, A0A2P2CLH2, O22769, Q9FNN5, Q9FGI6, Q42599, Q9SK66, Q9FJW4, Q9M9M6, Q9FIJ2, O80800, Q9FLX7, Q9LHI0, Q8RWA7, Q9M9M9, Q9SD78
- Ligands
- SF4, FES, FMN, NDP, 8Q1, ZN
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 17 distinct chains · 37% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial (EC 7.1.1.2) | protein | 157 | 46% helix, 13% strand | Q42577 |
| C | NADH dehydrogenase [ubiquinone] iron-sulfur protein 3 (EC 7.1.1.2) | protein | 185 | 19% helix, 30% strand | Q95748 |
| D | NADH dehydrogenase subunit 7 | protein | 385 | 48% helix, 11% strand | A0A2P2CLH2 |
| E | NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial (EC 7.1.1.2) | protein | 192 | 39% helix, 11% strand | O22769 |
| F | NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (EC 7.1.1.2) | protein | 434 | 45% helix, 13% strand | Q9FNN5 |
| G | NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial (EC 7.1.1.2) | protein | 688 | 30% helix, 17% strand | Q9FGI6 |
| I | NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-a, mitochondrial (EC 7.1.1.2) | protein | 165 | 33% helix, 16% strand | Q42599 |
| P | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial | protein | 332 | 35% helix, 12% strand | Q9SK66 |
| Q | NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial | protein | 119 | 26% helix, 20% strand | Q9FJW4 |
| R | NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial | protein | 62 | 13% helix, 27% strand | Q9M9M6 |
| S | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 | protein | 93 | 42% helix, 23% strand | Q9FIJ2 |
| U | Acyl carrier protein 2, mitochondrial | protein | 83 | 45% helix, 0% strand | O80800 |
| V | Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial | protein | 140 | 54% helix, 4% strand | Q9FLX7 |
| W | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 | protein | 112 | 63% helix, 0% strand | Q9LHI0 |
| Z | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-a | protein | 27 | 0% helix, 0% strand | Q8RWA7 |
| q | Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 | protein | 65 | 17% helix, 20% strand | Q9M9M9 |
| r | Furry | protein | 10 | 0% helix, 40% strand | Q9SD78 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 6 copies · chains B, D, F, G, I
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains E, G
- FMN · Flavin mononucleotide · ligand · chains F
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains B, P
- 8Q1 · S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy) butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate · ligand · chains U, W
- ZN · Zinc ion · metal · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1110 | 0.82 | 0.83 | 109 | NDP |
| 2 | 1155 | 0.82 | 0.83 | 130 | empty |
| 3 | 1170 | 0.81 | 0.82 | 114 | 8Q1 |
| 4 | 588 | 0.80 | 0.86 | 48 | empty |
| 5 | 443 | 0.80 | 0.88 | 58 | empty |
Interfaces
42 interfaces between chains.
- C–D · 2191 Ų buried · 28 hydrogen bonds · protein-protein
- G–Q · 2009 Ų buried · 18 hydrogen bonds · protein-protein
- C–V · 1994 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 1913 Ų buried · 25 hydrogen bonds · protein-protein
- D–I · 1695 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent, 2 disulfide (covalent ligand, disulfide).
Compared structures
- 7AQR · Cryo-EM structure of Arabidopsis thaliana Complex-I (peripheral arm) · the same entry in another collection · chain S against S, 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 Q42577
- Every structure of UniProt Q95748
- Every structure of UniProt A0A2P2CLH2
- Every structure of UniProt O22769
- Every structure of UniProt Q9FNN5
- Every structure of UniProt Q9FGI6
- Every structure of UniProt Q42599
- Every structure of UniProt Q9SK66
- Every structure of UniProt Q9FJW4
- Every structure of UniProt Q9M9M6
- Every structure of UniProt Q9FIJ2
- Every structure of UniProt O80800
- Every structure of UniProt Q9FLX7
- Every structure of UniProt Q9LHI0
- Every structure of UniProt Q8RWA7
- Every structure of UniProt Q9M9M9
- Every structure of UniProt Q9SD78
- Elsewhere: RCSB PDB 7AQR · PDBe 7AQR · UniProt Q42577 · UniProt Q95748 · UniProt A0A2P2CLH2 · UniProt O22769 · UniProt Q9FNN5 · UniProt Q9FGI6 · UniProt Q42599 · UniProt Q9SK66 · UniProt Q9FJW4 · UniProt Q9M9M6 · UniProt Q9FIJ2 · UniProt O80800 · UniProt Q9FLX7 · UniProt Q9LHI0 · UniProt Q8RWA7 · UniProt Q9M9M9 · UniProt Q9SD78
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