Research workbench
Complex I with NADH, OPEN2
Analyse Complex I with NADH, OPEN2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZKI
- Type
- protein
- Length
- 8,163 residues
- Chains
- 45
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial; Mitochondrial complex I…
- EC
- 1.6.99.3, 7.1.1.2
- UniProt
- W5PUX0, W5NRY1, W5QB34, W5PB27, O78753, O78747, O78757, O78754, O78756, O78755, O78748, W5PAR2, W5QHN8, W5NQT7, W5PYA5, W5PE07, W5PI58, W5QAH8, W5PNX7, W5QC06, W5P0I2, B9VGZ9, W5QBF5, W5QFF9, W5NYM7, W5Q5T4, W5P9Q8, W5QF73, W5PZE3, W5P5V3, W5PGA3, W5PVD7, W5Q1B0, W5PWF1
- Ligands
- 3PE, CDL, SF4, PC1, FES, ZMP, FMN, NAI, DCQ, NDP, AMP, MYR, K, ZN
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · 45 distinct chains · 51% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (EC 1.6.99.3, 7.1.1.2) | protein | 430 | 46% helix, 14% strand | W5PUX0 |
| 2 | Mitochondrial complex I, 24 kda subunit | protein | 213 | 34% helix, 11% strand | W5NRY1 |
| 3 | NADH:UBIQUINONE oxidoreductase core subunit S1 | protein | 688 | 31% helix, 18% strand | W5QB34 |
| 4 | Mitochondrial complex I, 49 kda subunit | protein | 426 | 47% helix, 13% strand | — |
| 5 | NADH:UBIQUINONE oxidoreductase core subunit S3 | protein | 208 | 22% helix, 27% strand | W5PB27 |
| 6 | Mitochondrial complex I, psst subunit | protein | 156 | 46% helix, 13% strand | — |
| 9 | Mitochondrial complex I, tyky subunit | protein | 176 | 37% helix, 17% strand | — |
| A | NADH-ubiquinone oxidoreductase chain 3 (EC 7.1.1.2) | protein | 104 | 70% helix, 0% strand | O78753 |
| H | NADH-ubiquinone oxidoreductase chain 1 (EC 7.1.1.2) | protein | 318 | 64% helix, 1% strand | O78747 |
| J | NADH-ubiquinone oxidoreductase chain 6 (EC 7.1.1.2) | protein | 169 | 68% 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 | 72% helix, 3% strand | O78755 |
| N | NADH-ubiquinone oxidoreductase chain 2 (EC 7.1.1.2) | protein | 347 | 75% 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 | 44% helix, 3% strand | W5PYA5 |
| Z | Mitochondrial complex I, pdsw subunit | protein | 171 | 65% helix, 3% strand | — |
| a | Mitochondrial complex I, 10 kda subunit | protein | 44 | 30% helix, 2% strand | — |
| b | Mitochondrial complex I, 13 kda subunit | protein | 95 | 15% helix, 23% strand | — |
| c | NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial | protein | 126 | 20% helix, 19% strand | W5PE07 |
| d | NADH:UBIQUINONE oxidoreductase subunit A9 | protein | 297 | 40% helix, 15% strand | W5PI58 |
| e | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 | protein | 86 | 42% helix, 30% strand | W5QAH8 |
| f | Mitochondrial complex I, B13 subunit | protein | 113 | 56% helix, 0% strand | W5PNX7 |
| g | NADH:UBIQUINONE oxidoreductase subunit A6 | protein | 114 | 61% helix, 2% strand | W5QC06 |
| h | Mitochondrial complex I, B14.5A subunit | protein | 96 | 15% helix, 6% strand | W5P0I2 |
| i | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 | protein | 145 | 23% helix, 13% strand | B9VGZ9 |
| j | Acyl carrier protein | protein | 82 | 48% helix, 0% strand | W5NQT7 |
| k | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial | protein | 320 | 50% 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 | 48% 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 | 58% helix, 1% strand | W5P9Q8 |
| p | NADH:UBIQUINONE oxidoreductase subunit B4 | protein | 128 | 55% helix, 2% strand | W5QF73 |
| q | Mitochondrial complex I, B16.6 subunit | protein | 139 | 56% helix, 1% strand | — |
| r | Mitochondrial complex I, B17 subunit | protein | 99 | 42% 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 | 55% helix, 0% strand | W5PGA3 |
| u | NADH:UBIQUINONE oxidoreductase subunit B2 | protein | 65 | 37% 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 | 44% helix, 0% strand | — |
| z | Mitochondrial complex I, mwfe subunit | protein | 70 | 61% helix, 0% strand | — |
Ligands and binding sites
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 14 copies · chains 4, L, M, N, 6, H, i, A, m, J, q, z, K, v, n, V, l, p, o
- CDL · Cardiolipin · ligand · 8 copies · chains L, M, W, w, N, V, p, Z, r, Y, o, y, x, k, H, h, i, z
- SF4 · Iron/sulfur cluster · ligand · 6 copies · chains 1, 3, 4, 6, 9
- PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 6 copies · chains 6, A, H, d, 4, 9, m, q, J, l, L, M, r, w, N, V
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains 1, 2, 3
- ZMP · S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy) butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate · ligand · 2 copies · chains X, t, g, j
- FMN · Flavin mononucleotide · ligand · chains 1
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · chains 1
- DCQ · 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione · ligand · chains 6, H
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains 6, d
- AMP · Adenosine monophosphate · ligand · chains k
- MYR · Myristic acid · ligand · chains L, s, v
- K · Potassium ion · metal · chains 3
- ZN · Zinc ion · metal · chains b
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 | 1188 | 0.90 | 0.92 | 161 | empty |
| 2 | 1002 | 0.89 | 0.90 | 100 | empty |
| 3 | 641 | 0.87 | 0.92 | 76 | empty |
| 4 | 1144 | 0.86 | 0.87 | 90 | 3PE |
| 5 | 862 | 0.86 | 0.88 | 98 | PC1, NDP |
Interfaces
199 interfaces between chains.
- 1–2 · 3121 Ų buried · 45 hydrogen bonds · protein-protein
- J–K · 2869 Ų buried · 12 hydrogen bonds · protein-protein
- A–H · 2786 Ų buried · 7 hydrogen bonds · protein-protein
- 4–5 · 2747 Ų buried · 41 hydrogen bonds · protein-protein
- L–M · 2409 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 modified, 5 disulfide, 1 covalent, 1 lipid (disulfide, formylation, nonstandard, covalent ligand, myristoylation, methylation).
Compared structures
- 6ZKI · Complex I with NADH, open2 · the same entry in another collection · chain A against A, 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 W5PUX0
- Every structure of UniProt W5NRY1
- Every structure of UniProt W5QB34
- Every structure of UniProt W5PB27
- 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 W5PE07
- Every structure of UniProt W5PI58
- Every structure of UniProt W5QAH8
- Every structure of UniProt W5PNX7
- Every structure of UniProt W5QC06
- Every structure of UniProt W5P0I2
- Every structure of UniProt B9VGZ9
- 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 6ZKI · PDBe 6ZKI · UniProt W5PUX0 · UniProt W5NRY1 · UniProt W5QB34 · UniProt W5PB27 · UniProt O78753 · UniProt O78747 · UniProt O78757 · UniProt O78754 · UniProt O78756 · UniProt O78755 · UniProt O78748 · UniProt W5PAR2 · UniProt W5QHN8 · UniProt W5NQT7 · UniProt W5PYA5 · UniProt W5PE07 · UniProt W5PI58 · UniProt W5QAH8 · UniProt W5PNX7 · UniProt W5QC06 · UniProt W5P0I2 · UniProt B9VGZ9 · 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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