Research workbench
Cryo-EM structure of respiratory complex I in the deactive state from Mus musculus at 3.2 A
Analyse Cryo-EM structure of respiratory complex I in the deactive state from Mus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AK5
- Type
- protein
- Length
- 8,069 residues
- Chains
- 45
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.17
- Source
- Mus musculus
- Molecule
- NADH-ubiquinone oxidoreductase chain 3; NADH dehydrogenase [ubiquinone] iron-sulfur…
- EC
- 7.1.1.2
- UniProt
- P03899, Q9DC70, Q9DCT2, Q91WD5, Q9D6J6, Q91YT0, Q91VD9, P03888, Q8K3J1, P03925, P03903, P03921, P03911, P03893, Q99LC3, Q9DC69, Q9CXZ1, P52503, Q9CQ75, Q9CR21, Q9CPP6, Q9CQZ5, Q9DCJ5, G5E814, Q9ERS2, O35683, Q9CQ91, Q9CQY9, Q9CQ54, Q99LY9, P0DN34, O09111, Q9CQH3, Q3UIU2, Q9CPU2, Q9CQZ6, Q9D6J5, Q9CQC7, Q9CQJ8, Q9CR61, Q9DCS9, Q7TMF3, Q9Z1P6, Q8BK30
- Ligands
- 3PE, SF4, CDL, PC1, FES, EHZ, FMN, ATP, NDP, ZN
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · resolution 3.17 · 45 distinct chains · 50% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NADH-ubiquinone oxidoreductase chain 3 (EC 7.1.1.2) | protein | 90 | 78% helix, 0% strand | P03899 |
| B | NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial (EC 7.1.1.2) | protein | 155 | 46% helix, 13% strand | Q9DC70 |
| C | NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial (EC 7.1.1.2) | protein | 206 | 20% helix, 27% strand | Q9DCT2 |
| D | NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial (EC 7.1.1.2) | protein | 419 | 47% helix, 13% strand | Q91WD5 |
| E | NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial (EC 7.1.1.2) | protein | 210 | 35% helix, 10% strand | Q9D6J6 |
| F | NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (EC 7.1.1.2) | protein | 428 | 45% helix, 13% strand | Q91YT0 |
| G | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial (EC 7.1.1.2) | protein | 687 | 31% helix, 17% strand | Q91VD9 |
| H | NADH-ubiquinone oxidoreductase chain 1 (EC 7.1.1.2) | protein | 308 | 67% helix, 0% strand | P03888 |
| I | NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial (EC 7.1.1.2) | protein | 178 | 33% helix, 16% strand | Q8K3J1 |
| J | NADH-ubiquinone oxidoreductase chain 6 (EC 7.1.1.2) | protein | 171 | 71% helix, 0% strand | P03925 |
| K | NADH-ubiquinone oxidoreductase chain 4L (EC 7.1.1.2) | protein | 98 | 77% helix, 0% strand | P03903 |
| L | NADH-ubiquinone oxidoreductase chain 5 (EC 7.1.1.2) | protein | 606 | 72% helix, 4% strand | P03921 |
| M | NADH-ubiquinone oxidoreductase chain 4 (EC 7.1.1.2) | protein | 459 | 71% helix, 2% strand | P03911 |
| N | NADH-ubiquinone oxidoreductase chain 2 (EC 7.1.1.2) | protein | 344 | 77% helix, 1% strand | P03893 |
| O | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial | protein | 320 | 50% helix, 7% strand | Q99LC3 |
| P | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial | protein | 290 | 33% helix, 15% strand | Q9DC69 |
| Q | NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial | protein | 125 | 19% helix, 18% strand | Q9CXZ1 |
| R | NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial | protein | 94 | 11% helix, 18% strand | P52503 |
| S | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 | protein | 82 | 37% helix, 23% strand | Q9CQ75 |
| T | Acyl carrier protein, mitochondrial | protein | 73 | 59% helix, 0% strand | Q9CR21 |
| U | Acyl carrier protein, mitochondrial | protein | 88 | 51% helix, 0% strand | Q9CR21 |
| V | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 | protein | 112 | 53% helix, 0% strand | Q9CPP6 |
| W | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 | protein | 114 | 61% helix, 2% strand | Q9CQZ5 |
| X | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 | protein | 171 | 40% helix, 2% strand | Q9DCJ5 |
| Y | MCG5603 | protein | 140 | 74% helix, 0% strand | G5E814 |
| Z | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 | protein | 139 | 56% helix, 1% strand | Q9ERS2 |
| a | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 | protein | 68 | 62% helix, 0% strand | O35683 |
| b | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 | protein | 83 | 55% helix, 2% strand | Q9CQ91 |
| c | NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial | protein | 46 | 78% helix, 0% strand | Q9CQY9 |
| d | NADH dehydrogenase [ubiquinone] 1 subunit C2 | protein | 119 | 53% helix, 1% strand | Q9CQ54 |
| e | NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 | protein | 104 | 54% helix, 0% strand | Q99LY9 |
| f | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 | protein | 50 | 42% helix, 0% strand | P0DN34 |
| g | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial | protein | 101 | 46% helix, 1% strand | O09111 |
| h | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial | protein | 137 | 58% helix, 2% strand | Q9CQH3 |
| i | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 | protein | 96 | 47% helix, 4% strand | Q3UIU2 |
| j | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial | protein | 63 | 43% helix, 3% strand | Q9CPU2 |
| k | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 | protein | 78 | 53% helix, 0% strand | Q9CQZ6 |
| l | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial | protein | 156 | 24% helix, 4% strand | Q9D6J5 |
| m | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 | protein | 125 | 58% helix, 0% strand | Q9CQC7 |
| n | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 | protein | 176 | 47% helix, 0% strand | Q9CQJ8 |
| o | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 | protein | 114 | 50% helix, 1% strand | Q9CR61 |
| p | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 | protein | 168 | 65% helix, 2% strand | Q9DCS9 |
| q | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 | protein | 143 | 24% helix, 11% strand | Q7TMF3 |
| r | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 | protein | 96 | 15% helix, 6% strand | Q9Z1P6 |
| s | NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial | protein | 39 | 26% helix, 3% strand | Q8BK30 |
Ligands and binding sites
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 8 copies · chains A, H, J, Z, a, D, I, b, L, M, l, N, Y, g, O, d, f, h, i
- SF4 · Iron/sulfur cluster · ligand · 6 copies · chains B, D, F, G, I
- CDL · Cardiolipin · ligand · 4 copies · chains L, M, g, h, N, X, d, f, i, p, H, I, a, q, r
- PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 2 copies · chains B, H, q, I, Z, r
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains E, F, G
- EHZ · ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate · ligand · 2 copies · chains T, W, U, n
- FMN · Flavin mononucleotide · ligand · chains F
- ATP · Adenosine-5'-triphosphate · ligand · chains O
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains B, P
- 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 | 1170 | 0.89 | 0.90 | 124 | 3PE |
| 2 | 1071 | 0.89 | 0.91 | 127 | empty |
| 3 | 820 | 0.88 | 0.91 | 90 | empty |
| 4 | 992 | 0.88 | 0.89 | 136 | EHZ |
| 5 | 960 | 0.86 | 0.87 | 128 | 3PE, CDL |
Interfaces
196 interfaces between chains.
- E–F · 2923 Ų buried · 31 hydrogen bonds · protein-protein
- J–K · 2760 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 2724 Ų buried · 29 hydrogen bonds · protein-protein
- A–H · 2485 Ų buried · 6 hydrogen bonds · protein-protein
- L–M · 2340 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 modified, 5 disulfide, 2 covalent (formylation, disulfide, covalent ligand, nonstandard, acetylation, methylation).
Compared structures
- 7AK5 · Cryo-EM structure of respiratory complex I in the deactive state from mus musculus at 3.2… · 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 P03899
- Every structure of UniProt Q9DC70
- Every structure of UniProt Q9DCT2
- Every structure of UniProt Q91WD5
- Every structure of UniProt Q9D6J6
- Every structure of UniProt Q91YT0
- Every structure of UniProt Q91VD9
- Every structure of UniProt P03888
- Every structure of UniProt Q8K3J1
- Every structure of UniProt P03925
- Every structure of UniProt P03903
- Every structure of UniProt P03921
- Every structure of UniProt P03911
- Every structure of UniProt P03893
- Every structure of UniProt Q99LC3
- Every structure of UniProt Q9DC69
- Every structure of UniProt Q9CXZ1
- Every structure of UniProt P52503
- Every structure of UniProt Q9CQ75
- Every structure of UniProt Q9CR21
- Every structure of UniProt Q9CPP6
- Every structure of UniProt Q9CQZ5
- Every structure of UniProt Q9DCJ5
- Every structure of UniProt G5E814
- Every structure of UniProt Q9ERS2
- Every structure of UniProt O35683
- Every structure of UniProt Q9CQ91
- Every structure of UniProt Q9CQY9
- Every structure of UniProt Q9CQ54
- Every structure of UniProt Q99LY9
- Every structure of UniProt P0DN34
- Every structure of UniProt O09111
- Every structure of UniProt Q9CQH3
- Every structure of UniProt Q3UIU2
- Every structure of UniProt Q9CPU2
- Every structure of UniProt Q9CQZ6
- Every structure of UniProt Q9D6J5
- Every structure of UniProt Q9CQC7
- Every structure of UniProt Q9CQJ8
- Every structure of UniProt Q9CR61
- Every structure of UniProt Q9DCS9
- Every structure of UniProt Q7TMF3
- Every structure of UniProt Q9Z1P6
- Every structure of UniProt Q8BK30
- Elsewhere: RCSB PDB 7AK5 · PDBe 7AK5 · UniProt P03899 · UniProt Q9DC70 · UniProt Q9DCT2 · UniProt Q91WD5 · UniProt Q9D6J6 · UniProt Q91YT0 · UniProt Q91VD9 · UniProt P03888 · UniProt Q8K3J1 · UniProt P03925 · UniProt P03903 · UniProt P03921 · UniProt P03911 · UniProt P03893 · UniProt Q99LC3 · UniProt Q9DC69 · UniProt Q9CXZ1 · UniProt P52503 · UniProt Q9CQ75 · UniProt Q9CR21 · UniProt Q9CPP6 · UniProt Q9CQZ5 · UniProt Q9DCJ5 · UniProt G5E814 · UniProt Q9ERS2 · UniProt O35683 · UniProt Q9CQ91 · UniProt Q9CQY9 · UniProt Q9CQ54 · UniProt Q99LY9 · UniProt P0DN34 · UniProt O09111 · UniProt Q9CQH3 · UniProt Q3UIU2 · UniProt Q9CPU2 · UniProt Q9CQZ6 · UniProt Q9D6J5 · UniProt Q9CQC7 · UniProt Q9CQJ8 · UniProt Q9CR61 · UniProt Q9DCS9 · UniProt Q7TMF3 · UniProt Q9Z1P6 · UniProt Q8BK30
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.