MolNFT v1 · #173173 · protein
Cryo-EM structure of arabidopsis thaliana complex-I (open conformation)
7AR7 · NADH-ubiquinone oxidoreductase chain 3: “Cryo-EM structure of arabidopsis thaliana complex-I (open conformation)”. Electron microscopy, 13 ligands (SF4, PTY, FES), 20 pockets (best druggability 0.86). MolNFT v1 #173173 on GenesisL1…
- PDB
- 7AR7
- Type
- protein
- Length
- 7,594 residues
- Chains
- 46
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH-ubiquinone oxidoreductase chain 3; NADH dehydrogenase [ubiquinone] iron-sulfur…
- EC
- 7.1.1.2, 4.2.1.-
- UniProt
- P92533, Q42577, Q95748, P93306, O22769, Q9FNN5, Q9FGI6, P92558, Q42599, A0A2P2CLG1, Q04614, P29388, P93313, O05000, Q9SK66, Q9FJW4, Q9M9M6, Q9FIJ2, P53665, O80800, Q9FLX7, Q9LHI0, Q8LGE7, Q8RWA7, Q9C9Z5, Q9ZPY5, Q8VZT9, Q94AL6, O82238, Q84W12, Q9SLC8, Q9FYF8, Q8LDK3, O64725, Q9FGK0, Q9SIQ8, Q945M1, Q9SKC9, Q94C12, Q9M9M9, Q9ZUX4, Q9SMN1, Q9C6B3, Q9FWR5
- Ligands
- SF4, PTY, FES, PC7, 8Q1, FMN, UQ9, LMN, NDP, PGT, PSF, T7X, ZN
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 46 distinct chains · 49% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NADH-ubiquinone oxidoreductase chain 3 (EC 7.1.1.2) | protein | 92 | 78% helix, 0% strand | P92533 |
| B | NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial (EC 7.1.1.2) | protein | 157 | 45% helix, 11% strand | Q42577 |
| C | NADH dehydrogenase [ubiquinone] iron-sulfur protein 3 (EC 7.1.1.2) | protein | 185 | 18% helix, 27% strand | Q95748 |
| D | NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 (EC 7.1.1.2) | protein | 385 | 48% helix, 10% strand | P93306 |
| E | NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial (EC 7.1.1.2) | protein | 192 | 40% helix, 10% strand | O22769 |
| F | NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (EC 7.1.1.2) | protein | 434 | 44% helix, 12% strand | Q9FNN5 |
| G | NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial (EC 7.1.1.2) | protein | 688 | 29% helix, 13% strand | Q9FGI6 |
| H | NADH-ubiquinone oxidoreductase chain 1 (EC 7.1.1.2) | protein | 324 | 61% helix, 0% strand | P92558 |
| I | NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-a, mitochondrial (EC 7.1.1.2) | protein | 169 | 33% helix, 16% strand | Q42599 |
| J | NADH-ubiquinone oxidoreductase chain 6 (EC 7.1.1.2) | protein | 138 | 68% helix, 0% strand | A0A2P2CLG1 |
| K | NADH-ubiquinone oxidoreductase chain 4L (EC 7.1.1.2) | protein | 88 | 85% helix, 0% strand | Q04614 |
| L | NADH-ubiquinone oxidoreductase chain 5 (EC 7.1.1.2) | protein | 615 | 67% helix, 3% strand | P29388 |
| M | NADH-ubiquinone oxidoreductase chain 4 (EC 7.1.1.2) | protein | 487 | 70% helix, 3% strand | P93313 |
| N | NADH-ubiquinone oxidoreductase chain 2 (EC 7.1.1.2) | protein | 488 | 72% helix, 1% strand | O05000 |
| P | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial | protein | 331 | 35% helix, 15% strand | Q9SK66 |
| Q | NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial | protein | 119 | 22% helix, 17% strand | Q9FJW4 |
| R | NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial | protein | 62 | 16% helix, 27% strand | Q9M9M6 |
| S | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 | protein | 93 | 32% helix, 16% strand | Q9FIJ2 |
| T | Acyl carrier protein 1, mitochondrial | protein | 84 | 42% helix, 2% strand | P53665 |
| U | Acyl carrier protein 2, mitochondrial | protein | 83 | 48% helix, 0% strand | O80800 |
| V | Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial | protein | 140 | 55% helix, 3% strand | Q9FLX7 |
| W | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 | protein | 108 | 63% helix, 0% strand | Q9LHI0 |
| X | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B | protein | 96 | 70% helix, 0% strand | Q8LGE7 |
| Z | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-a | protein | 125 | 50% helix, 0% strand | Q8RWA7 |
| a | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 | protein | 58 | 78% helix, 0% strand | Q9C9Z5 |
| b | AT2G46540/F11C10.23 | protein | 40 | 90% helix, 0% strand | Q9ZPY5 |
| c | Transmembrane protein | protein | 76 | 32% helix, 0% strand | Q8VZT9 |
| d | Excitatory amino acid transporter | protein | 75 | 75% helix, 0% strand | Q94AL6 |
| e | NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-a | protein | 64 | 59% helix, 0% strand | O82238 |
| f | AT4G16450 | protein | 100 | 61% helix, 0% strand | Q84W12 |
| g | Esss subunit of NADH:UBIQUINONE oxidoreductase (complex I) protein | protein | 72 | 51% helix, 0% strand | Q9SLC8 |
| i | AT1G67350 | protein | 85 | 54% helix, 0% strand | Q9FYF8 |
| j | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2 | protein | 51 | 57% helix, 8% strand | Q8LDK3 |
| k | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-a | protein | 47 | 60% helix, 0% strand | O64725 |
| l | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial | protein | 46 | 67% helix, 0% strand | Q9FGK0 |
| m | AT2G31490 protein | protein | 67 | 70% helix, 0% strand | Q9SIQ8 |
| n | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 | protein | 109 | 50% helix, 1% strand | Q945M1 |
| o | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 | protein | 80 | 61% helix, 0% strand | Q9SKC9 |
| p | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-B | protein | 93 | 57% helix, 0% strand | Q94C12 |
| q | Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 | protein | 63 | 11% helix, 16% strand | Q9M9M9 |
| r | B14.5A | protein | 10 | 0% helix, 40% strand | — |
| u | Unknown | protein | 30 | 80% helix, 0% strand | — |
| v | Uncharacterized protein AT2G27730, mitochondrial | protein | 30 | 77% helix, 0% strand | Q9ZUX4 |
| x | Gamma carbonic anhydrase-like 2, mitochondrial | protein | 214 | 14% helix, 25% strand | Q9SMN1 |
| y | Gamma carbonic anhydrase 2, mitochondrial (EC 4.2.1.-) | protein | 268 | 29% helix, 16% strand | Q9C6B3 |
| z | Gamma carbonic anhydrase 1, mitochondrial (EC 4.2.1.-) | protein | 233 | 26% helix, 18% strand | Q9FWR5 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 6 copies · chains B, D, F, G, I
- PTY · Phosphatidylethanolamine · ligand · 3 copies · chains D, H, I, Z, b, M, g, N, d
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains E, G
- PC7 · (7S)-4-hydroxy-N,N,N-trimethyl-9-oxo-7-[(palmitoyloxy) methyl]-3,5,8-trioxa-4-phosphahexacosan-1-aminium 4-oxide · ligand · 2 copies · chains L, M, c, N, f, v
- 8Q1 · S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy) butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate · ligand · 2 copies · chains U, W, L, T, n
- FMN · Flavin mononucleotide · ligand · chains F
- UQ9 · Ubiquinone-9 · ligand · chains B, H, a
- LMN · Lauryl Maltose Neopentyl Glycol · ligand · chains M, N, d
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains B, P
- PGT · (1S)-2-{[{[(2R)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate · ligand · chains N, f, y, z
- PSF · 1,2-dicaproyl-sn-phosphatidyl-L-serine · ligand · chains N, d, x, z
- T7X · Phosphatidylinositol · ligand · chains f, v, y, z
- ZN · Zinc ion · metal · 2 copies · chains R, y, z
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 | 1082 | 0.86 | 0.86 | 105 | empty |
| 2 | 803 | 0.86 | 0.88 | 90 | NDP |
| 3 | 747 | 0.85 | 0.89 | 89 | empty |
| 4 | 961 | 0.85 | 0.86 | 75 | empty |
| 5 | 508 | 0.84 | 0.91 | 61 | empty |
Interfaces
152 interfaces between chains.
- x–z · 2650 Ų buried · 29 hydrogen bonds · protein-protein
- y–z · 2624 Ų buried · 25 hydrogen bonds · protein-protein
- A–H · 2593 Ų buried · 4 hydrogen bonds · protein-protein
- x–y · 2523 Ų buried · 24 hydrogen bonds · protein-protein
- L–M · 2434 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 covalent, 5 disulfide (covalent ligand, disulfide).
Compared structures
- 7AR7 · Cryo-EM structure of Arabidopsis thaliana complex-I (open conformation) · the same entry in another collection · chain I against I, 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 P92533
- Every structure of UniProt Q42577
- Every structure of UniProt Q95748
- Every structure of UniProt P93306
- Every structure of UniProt O22769
- Every structure of UniProt Q9FNN5
- Every structure of UniProt Q9FGI6
- Every structure of UniProt P92558
- Every structure of UniProt Q42599
- Every structure of UniProt A0A2P2CLG1
- Every structure of UniProt Q04614
- Every structure of UniProt P29388
- Every structure of UniProt P93313
- Every structure of UniProt O05000
- Every structure of UniProt Q9SK66
- Every structure of UniProt Q9FJW4
- Every structure of UniProt Q9M9M6
- Every structure of UniProt Q9FIJ2
- Every structure of UniProt P53665
- Every structure of UniProt O80800
- Every structure of UniProt Q9FLX7
- Every structure of UniProt Q9LHI0
- Every structure of UniProt Q8LGE7
- Every structure of UniProt Q8RWA7
- Every structure of UniProt Q9C9Z5
- Every structure of UniProt Q9ZPY5
- Every structure of UniProt Q8VZT9
- Every structure of UniProt Q94AL6
- Every structure of UniProt O82238
- Every structure of UniProt Q84W12
- Every structure of UniProt Q9SLC8
- Every structure of UniProt Q9FYF8
- Every structure of UniProt Q8LDK3
- Every structure of UniProt O64725
- Every structure of UniProt Q9FGK0
- Every structure of UniProt Q9SIQ8
- Every structure of UniProt Q945M1
- Every structure of UniProt Q9SKC9
- Every structure of UniProt Q94C12
- Every structure of UniProt Q9M9M9
- Every structure of UniProt Q9ZUX4
- Every structure of UniProt Q9SMN1
- Every structure of UniProt Q9C6B3
- Every structure of UniProt Q9FWR5
- Elsewhere: RCSB PDB 7AR7 · PDBe 7AR7 · UniProt P92533 · UniProt Q42577 · UniProt Q95748 · UniProt P93306 · UniProt O22769 · UniProt Q9FNN5 · UniProt Q9FGI6 · UniProt P92558 · UniProt Q42599 · UniProt A0A2P2CLG1 · UniProt Q04614 · UniProt P29388 · UniProt P93313 · UniProt O05000 · UniProt Q9SK66 · UniProt Q9FJW4 · UniProt Q9M9M6 · UniProt Q9FIJ2 · UniProt P53665 · UniProt O80800 · UniProt Q9FLX7 · UniProt Q9LHI0 · UniProt Q8LGE7 · UniProt Q8RWA7 · UniProt Q9C9Z5 · UniProt Q9ZPY5 · UniProt Q8VZT9 · UniProt Q94AL6 · UniProt O82238 · UniProt Q84W12 · UniProt Q9SLC8 · UniProt Q9FYF8 · UniProt Q8LDK3 · UniProt O64725 · UniProt Q9FGK0 · UniProt Q9SIQ8 · UniProt Q945M1 · UniProt Q9SKC9 · UniProt Q94C12 · UniProt Q9M9M9 · UniProt Q9ZUX4 · UniProt Q9SMN1 · UniProt Q9C6B3 · UniProt Q9FWR5
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