MolNFT v1 · #171896 · protein
Membrane domain of open complex I during turnover
6ZKA · NADH-ubiquinone oxidoreductase chain 3: “Membrane domain of open complex I during turnover”. Electron microscopy, 7 ligands (3PE, CDL, PC1), 20 pockets (best druggability 0.90). MolNFT v1 #171896 on GenesisL1: 3D structure, binding…
- PDB
- 6ZKA
- Type
- protein
- Length
- 4,694 residues
- Chains
- 29
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH-ubiquinone oxidoreductase chain 3; NADH-ubiquinone oxidoreductase chain 1…
- EC
- 7.1.1.2
- UniProt
- O78753, O78747, O78757, O78754, O78756, O78755, O78748, W5PAR2, W5QHN8, W5NQT7, W5PYA5, W5QBF5, W5QFF9, W5NYM7, W5Q5T4, W5P9Q8, W5QF73, W5PZE3, W5P5V3, W5PGA3, W5PVD7, W5Q1B0, W5PWF1
- Ligands
- 3PE, CDL, PC1, DCQ, ZMP, AMP, MYR
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · 29 distinct chains · 63% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NADH-ubiquinone oxidoreductase chain 3 (EC 7.1.1.2) | protein | 97 | 72% helix, 0% strand | O78753 |
| H | NADH-ubiquinone oxidoreductase chain 1 (EC 7.1.1.2) | protein | 313 | 65% helix, 1% strand | O78747 |
| J | NADH-ubiquinone oxidoreductase chain 6 (EC 7.1.1.2) | protein | 167 | 71% helix, 4% strand | O78757 |
| K | NADH-ubiquinone oxidoreductase chain 4L (EC 7.1.1.2) | protein | 98 | 82% helix, 2% strand | O78754 |
| L | NADH-ubiquinone oxidoreductase chain 5 (EC 7.1.1.2) | protein | 606 | 74% helix, 5% strand | O78756 |
| M | NADH-ubiquinone oxidoreductase chain 4 (EC 7.1.1.2) | protein | 459 | 74% helix, 3% strand | O78755 |
| N | NADH-ubiquinone oxidoreductase chain 2 (EC 7.1.1.2) | protein | 347 | 74% helix, 2% strand | O78748 |
| V | Mitochondrial complex I, B14.7 subunit | protein | 140 | 78% helix, 0% strand | W5PAR2 |
| W | NADH:UBIQUINONE oxidoreductase subunit B5 | protein | 139 | 60% helix, 3% strand | W5QHN8 |
| X | Acyl carrier protein | protein | 87 | 51% helix, 0% strand | W5NQT7 |
| Y | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 | protein | 171 | 46% helix, 2% strand | W5PYA5 |
| Z | Mitochondrial complex I, pdsw subunit | protein | 171 | 67% helix, 3% strand | — |
| k | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial | protein | 320 | 51% helix, 8% strand | W5QBF5 |
| l | NADH:UBIQUINONE oxidoreductase subunit S5 | protein | 105 | 59% helix, 0% strand | W5QFF9 |
| m | NADH:UBIQUINONE oxidoreductase subunit A3 | protein | 80 | 53% helix, 3% strand | W5NYM7 |
| n | NADH:UBIQUINONE oxidoreductase subunit B3 | protein | 79 | 56% helix, 0% strand | W5Q5T4 |
| o | NADH dehydrogenase [ubiquinone] 1 subunit C2 | protein | 120 | 56% helix, 1% strand | W5P9Q8 |
| p | NADH:UBIQUINONE oxidoreductase subunit B4 | protein | 128 | 58% helix, 1% strand | W5QF73 |
| q | Mitochondrial complex I, B16.6 subunit | protein | 139 | 60% helix, 1% strand | — |
| r | Mitochondrial complex I, B17 subunit | protein | 99 | 41% helix, 7% strand | W5PZE3 |
| s | NADH:UBIQUINONE oxidoreductase subunit B7 | protein | 122 | 56% helix, 1% strand | W5P5V3 |
| t | NADH:UBIQUINONE oxidoreductase subunit B9 | protein | 177 | 56% helix, 0% strand | W5PGA3 |
| u | NADH:UBIQUINONE oxidoreductase subunit B2 | protein | 65 | 54% helix, 3% strand | W5PVD7 |
| v | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial | protein | 155 | 29% helix, 5% strand | W5Q1B0 |
| w | Mitochondrial complex I, esss subunit | protein | 101 | 54% helix, 1% strand | W5PWF1 |
| x | Mitochondrial complex I, kfyi subunit | protein | 49 | 67% helix, 0% strand | — |
| y | Mitochondrial complex I, mnll subunit | protein | 50 | 48% helix, 0% strand | — |
| z | Mitochondrial complex I, mwfe subunit | protein | 70 | 60% helix, 0% strand | — |
| 4 | Mitochondrial complex I, ND4L subunit | protein | 40 | 25% helix, 3% strand | — |
Ligands and binding sites
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 12 copies · chains A, H, J, q, z, K, L, M, N, 4, v, n, V, l, m, o, p
- CDL · Cardiolipin · ligand · 7 copies · chains L, M, W, w, N, k, o, V, p, Z, r, Y, y, x
- PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 5 copies · chains A, J, l, H, m, q, L, M, r, w, N, V
- DCQ · 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione · ligand · chains H
- ZMP · S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy) butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate · ligand · chains X, t
- AMP · Adenosine monophosphate · ligand · chains k
- MYR · Myristic acid · ligand · chains L, s, v
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 | 1085 | 0.90 | 0.91 | 126 | 3PE |
| 2 | 1197 | 0.88 | 0.90 | 134 | empty |
| 3 | 839 | 0.86 | 0.87 | 104 | CDL |
| 4 | 334 | 0.85 | 0.95 | 56 | empty |
| 5 | 785 | 0.85 | 0.88 | 74 | 3PE |
Interfaces
121 interfaces between chains.
- J–K · 2842 Ų buried · 13 hydrogen bonds · protein-protein
- A–H · 2704 Ų buried · 5 hydrogen bonds · protein-protein
- L–M · 2392 Ų buried · 12 hydrogen bonds · protein-protein
- p–v · 2020 Ų buried · 35 hydrogen bonds · protein-protein
- Y–q · 1917 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 5 modified, 1 covalent, 1 lipid (disulfide, formylation, covalent ligand, myristoylation, nonstandard, phosphorylation).
Compared structures
- O78748 · AlphaFold monomer V2.0 prediction for NADH-ubiquinone oxidoreductase chain 2 (O78748) · a predicted model of the same protein · chain N against A, TM-score 0.99
- O78755 · AlphaFold monomer V2.0 prediction for NADH-ubiquinone oxidoreductase chain 4 (O78755) · a predicted model of the same protein · chain M against A, TM-score 0.99
- O78747 · AlphaFold monomer V2.0 prediction for NADH-ubiquinone oxidoreductase chain 1 (O78747) · a predicted model of the same protein · chain H against A, TM-score 0.98
- O78756 · AlphaFold monomer V2.0 prediction for NADH-ubiquinone oxidoreductase chain 5 (O78756) · a predicted model of the same protein · chain L against A, TM-score 0.98
- O78754 · AlphaFold monomer V2.0 prediction for NADH-ubiquinone oxidoreductase chain 4L (O78754) · a predicted model of the same protein · chain K against A, TM-score 0.95
- O78757 · AlphaFold monomer V2.0 prediction for NADH-ubiquinone oxidoreductase chain 6 (O78757) · a predicted model of the same protein · chain J against A, TM-score 0.90
- O78753 · AlphaFold monomer V2.0 prediction for NADH-ubiquinone oxidoreductase chain 3 (O78753) · a predicted model of the same protein · chain A against A, TM-score 0.81
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 O78753
- Every structure of UniProt O78747
- Every structure of UniProt O78757
- Every structure of UniProt O78754
- Every structure of UniProt O78756
- Every structure of UniProt O78755
- Every structure of UniProt O78748
- Every structure of UniProt W5PAR2
- Every structure of UniProt W5QHN8
- Every structure of UniProt W5NQT7
- Every structure of UniProt W5PYA5
- Every structure of UniProt W5QBF5
- Every structure of UniProt W5QFF9
- Every structure of UniProt W5NYM7
- Every structure of UniProt W5Q5T4
- Every structure of UniProt W5P9Q8
- Every structure of UniProt W5QF73
- Every structure of UniProt W5PZE3
- Every structure of UniProt W5P5V3
- Every structure of UniProt W5PGA3
- Every structure of UniProt W5PVD7
- Every structure of UniProt W5Q1B0
- Every structure of UniProt W5PWF1
- Elsewhere: RCSB PDB 6ZKA · PDBe 6ZKA · UniProt O78753 · UniProt O78747 · UniProt O78757 · UniProt O78754 · UniProt O78756 · UniProt O78755 · UniProt O78748 · UniProt W5PAR2 · UniProt W5QHN8 · UniProt W5NQT7 · UniProt W5PYA5 · UniProt W5QBF5 · UniProt W5QFF9 · UniProt W5NYM7 · UniProt W5Q5T4 · UniProt W5P9Q8 · UniProt W5QF73 · UniProt W5PZE3 · UniProt W5P5V3 · UniProt W5PGA3 · UniProt W5PVD7 · UniProt W5Q1B0 · UniProt W5PWF1
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