MolNFT v1 · #171895 · protein
Peripheral domain of open complex I during turnover
6ZK9 · NADH dehydrogenase [ubiquinone] flavoprotein 1…: “Peripheral domain of open complex I during turnover”. Electron microscopy, 11 ligands (SF4, FES, PC1), 20 pockets (best druggability 0.89). MolNFT v1 #171895 on GenesisL1: 3D…
- PDB
- 6ZK9
- Type
- protein
- Length
- 3,480 residues
- Chains
- 18
- 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, W5PE07, W5PI58, W5QAH8, W5PNX7, W5QC06, W5P0I2, B9VGZ9, W5NQT7
- Ligands
- SF4, FES, PC1, 3PE, FMN, NAI, NDP, ZMP, CDL, K, ZN
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 18 distinct chains · 38% helix, 14% 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 | 47% helix, 13% strand | W5PUX0 |
| 2 | Mitochondrial complex I, 24 kda subunit | protein | 213 | 37% helix, 11% strand | W5NRY1 |
| 3 | NADH:UBIQUINONE oxidoreductase core subunit S1 | protein | 688 | 32% helix, 17% strand | W5QB34 |
| 4 | Mitochondrial complex I, 49 kda subunit | protein | 380 | 50% helix, 14% strand | — |
| 5 | NADH:UBIQUINONE oxidoreductase core subunit S3 | protein | 208 | 22% helix, 27% strand | W5PB27 |
| 6 | Mitochondrial complex I, psst subunit | protein | 156 | 49% helix, 13% strand | — |
| 9 | Mitochondrial complex I, tyky subunit | protein | 176 | 38% helix, 17% strand | — |
| a | Mitochondrial complex I, 10 kda subunit | protein | 44 | 36% helix, 2% strand | — |
| b | Mitochondrial complex I, 13 kda subunit | protein | 95 | 16% helix, 22% strand | — |
| c | NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial | protein | 126 | 21% helix, 20% strand | W5PE07 |
| d | NADH:UBIQUINONE oxidoreductase subunit A9 | protein | 297 | 39% helix, 15% strand | W5PI58 |
| e | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 | protein | 86 | 43% helix, 30% strand | W5QAH8 |
| f | Mitochondrial complex I, B13 subunit | protein | 113 | 57% 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, 7% strand | W5P0I2 |
| i | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 | protein | 145 | 24% helix, 12% strand | B9VGZ9 |
| j | Acyl carrier protein | protein | 82 | 48% helix, 0% strand | W5NQT7 |
| q | Mitochondrial complex I, B16.6 subunit | protein | 31 | 13% helix, 3% strand | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 6 copies · chains 1, 3, 4, 6, 9
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains 1, 2, 3
- PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 2 copies · chains 6, d, 4, 9, q
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 2 copies · chains 6, i
- FMN · Flavin mononucleotide · ligand · chains 1
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · chains 1
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains 6, d
- ZMP · S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy) butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate · ligand · chains g, j
- CDL · Cardiolipin · ligand · chains h, i
- 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 | 1160 | 0.89 | 0.91 | 133 | empty |
| 2 | 820 | 0.87 | 0.89 | 98 | ZMP |
| 3 | 379 | 0.83 | 0.92 | 50 | empty |
| 4 | 546 | 0.80 | 0.86 | 68 | NDP |
| 5 | 780 | 0.78 | 0.82 | 71 | FMN, NAI |
Interfaces
63 interfaces between chains.
- 1–2 · 3157 Ų buried · 44 hydrogen bonds · protein-protein
- 4–5 · 2754 Ų buried · 41 hydrogen bonds · protein-protein
- 4–9 · 2311 Ų buried · 56 hydrogen bonds · protein-protein
- 9–i · 2166 Ų buried · 37 hydrogen bonds · protein-protein
- 3–c · 2135 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation, nonstandard).
Compared structures
- 6ZK9 · Peripheral domain of open complex I during turnover · the same entry in another collection · chain 1 against 1, 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 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 W5NQT7
- Elsewhere: RCSB PDB 6ZK9 · PDBe 6ZK9 · UniProt W5PUX0 · UniProt W5NRY1 · UniProt W5QB34 · UniProt W5PB27 · UniProt W5PE07 · UniProt W5PI58 · UniProt W5QAH8 · UniProt W5PNX7 · UniProt W5QC06 · UniProt W5P0I2 · UniProt B9VGZ9 · UniProt W5NQT7
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