MolNFT v2 · #212953 · protein
Respiratory complex Membrane domain of CI, focus-refined of type I, PERK -/- mouse under cold temperature
8IC4 · NADH dehydrogenase [ubiquinone] iron-sulfur protein 2…: “Respiratory complex Membrane domain of CI, focus-refined of type I, PERK -/- mouse under cold temperature”. Electron microscopy at 3.2, 5 ligands (3PE, CDL, ADP), 20 pockets…
- PDB
- 8IC4
- Type
- protein
- Length
- 3,804 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.2
- Source
- Mus musculus
- Molecule
- NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial; NADH-ubiquinone…
- EC
- 7.1.1.2
- UniProt
- Q91WD5, P03925, P03903, P03921, P03911, P03893, Q99LC3, Q9CR21, Q9DCJ5, G5E814, Q9CQY9, Q9CQ54, Q99LY9, P0DN34, O09111, Q9CQH3, Q3UIU2, Q9CPU2, Q9CQZ6, Q9D6J5, Q9CQC7, Q9CQJ8, Q9CR61, Q9DCS9
- Ligands
- 3PE, CDL, ADP, EHZ, ZN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · resolution 3.2 · 24 distinct chains · 60% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial (EC 7.1.1.2) | protein | 42 | 21% helix, 0% strand | Q91WD5 |
| J | NADH-ubiquinone oxidoreductase chain 6 (EC 7.1.1.2) | protein | 155 | 75% helix, 0% strand | P03925 |
| K | NADH-ubiquinone oxidoreductase chain 4L (EC 7.1.1.2) | protein | 96 | 78% helix, 0% strand | P03903 |
| L | NADH-ubiquinone oxidoreductase chain 5 (EC 7.1.1.2) | protein | 606 | 75% helix, 4% strand | P03921 |
| M | NADH-ubiquinone oxidoreductase chain 4 (EC 7.1.1.2) | protein | 459 | 69% helix, 1% 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 | 318 | 53% helix, 5% strand | Q99LC3 |
| U | Acyl carrier protein, mitochondrial | protein | 87 | 39% helix, 0% strand | Q9CR21 |
| X | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 | protein | 27 | 0% helix, 0% strand | Q9DCJ5 |
| Y | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 | protein | 139 | 78% helix, 0% strand | G5E814 |
| c | NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial | protein | 47 | 68% helix, 0% strand | Q9CQY9 |
| d | NADH dehydrogenase [ubiquinone] 1 subunit C2 | protein | 120 | 53% helix, 0% strand | Q9CQ54 |
| e | NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 | protein | 103 | 46% helix, 0% strand | Q99LY9 |
| f | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 | protein | 51 | 49% helix, 0% strand | P0DN34 |
| g | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial | protein | 99 | 44% helix, 0% strand | O09111 |
| h | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial | protein | 138 | 57% helix, 2% strand | Q9CQH3 |
| i | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 | protein | 91 | 37% helix, 8% strand | Q3UIU2 |
| j | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial | protein | 67 | 46% helix, 3% strand | Q9CPU2 |
| k | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 | protein | 69 | 55% helix, 0% strand | Q9CQZ6 |
| l | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial | protein | 155 | 28% helix, 5% strand | Q9D6J5 |
| m | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 | protein | 126 | 46% helix, 1% strand | Q9CQC7 |
| n | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 | protein | 177 | 45% helix, 0% strand | Q9CQJ8 |
| o | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 | protein | 121 | 58% helix, 1% strand | Q9CR61 |
| p | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 | protein | 167 | 54% helix, 2% strand | Q9DCS9 |
Ligands and binding sites
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 9 copies · chains D, L, M, N, J, j, k, o, l, g, Y, m, i
- CDL · Cardiolipin · ligand · 5 copies · chains L, M, h, N, d, Y, X, f, g, i, p
- ADP · Adenosine-5'-diphosphate · ligand · chains O
- EHZ · ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate · ligand · chains U, n
- ZN · Zinc ion · metal · chains L
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 | 1070 | 0.87 | 0.88 | 99 | empty |
| 2 | 1000 | 0.86 | 0.87 | 78 | empty |
| 3 | 981 | 0.84 | 0.85 | 89 | empty |
| 4 | 695 | 0.83 | 0.87 | 95 | CDL |
| 5 | 280 | 0.83 | 0.94 | 43 | empty |
Interfaces
94 interfaces between chains.
- J–K · 2475 Ų buried · 11 hydrogen bonds · protein-protein
- L–M · 2361 Ų buried · 6 hydrogen bonds · protein-protein
- l–m · 2081 Ų buried · 40 hydrogen bonds · protein-protein
- g–p · 1754 Ų buried · 21 hydrogen bonds · protein-protein
- L–l · 1711 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- P03911 · AlphaFold monomer V2.0 prediction for NADH-ubiquinone oxidoreductase chain 4 (P03911) · a predicted model of the same protein · chain M against A, TM-score 0.99
- Q99LC3 · AlphaFold monomer V2.0 prediction for NADH dehydrogenase [ubiquinone] 1 alpha subcomplex… · a predicted model of the same protein · chain O against A, TM-score 0.99
- Q9DCS9 · AlphaFold monomer V2.0 prediction for NADH dehydrogenase [ubiquinone] 1 beta subcomplex… · a predicted model of the same protein · chain p against A, TM-score 0.97
- Q9D6J5 · AlphaFold monomer V2.0 prediction for NADH dehydrogenase [ubiquinone] 1 beta subcomplex… · a predicted model of the same protein · chain l against A, TM-score 0.97
- Q9CQZ6 · AlphaFold monomer V2.0 prediction for NADH dehydrogenase [ubiquinone] 1 beta subcomplex… · a predicted model of the same protein · chain k against A, TM-score 0.96
- Q9CR61 · AlphaFold monomer V2.0 prediction for NADH dehydrogenase [ubiquinone] 1 beta subcomplex… · a predicted model of the same protein · chain o against A, TM-score 0.96
- Q9CQJ8 · AlphaFold monomer V2.0 prediction for NADH dehydrogenase [ubiquinone] 1 beta subcomplex… · a predicted model of the same protein · chain n against A, TM-score 0.96
- Q9CR21 · AlphaFold monomer V2.0 prediction for acyl carrier protein, mitochondrial (Q9CR21) · a predicted model of the same protein · chain U against A, TM-score 0.95
- Q9CQC7 · AlphaFold monomer V2.0 prediction for NADH dehydrogenase [ubiquinone] 1 beta subcomplex… · a predicted model of the same protein · chain m against A, TM-score 0.94
- Q9CQH3 · AlphaFold monomer V2.0 prediction for NADH dehydrogenase [ubiquinone] 1 beta subcomplex… · a predicted model of the same protein · chain h against A, TM-score 0.93
- Q9CQ54 · AlphaFold monomer V2.0 prediction for NADH dehydrogenase [ubiquinone] 1 subunit C2… · a predicted model of the same protein · chain d against A, TM-score 0.92
- Q99LY9 · AlphaFold monomer V2.0 prediction for NADH dehydrogenase [ubiquinone] iron-sulfur protein… · a predicted model of the same protein · chain e against A, TM-score 0.92
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 Q91WD5
- 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 Q9CR21
- Every structure of UniProt Q9DCJ5
- Every structure of UniProt G5E814
- 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
- Elsewhere: RCSB PDB 8IC4 · PDBe 8IC4 · UniProt Q91WD5 · UniProt P03925 · UniProt P03903 · UniProt P03921 · UniProt P03911 · UniProt P03893 · UniProt Q99LC3 · UniProt Q9CR21 · UniProt Q9DCJ5 · UniProt G5E814 · 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.