MolNFT v1 · #176268 · protein
Activity optimized complex I (closed form)
7DGZ · NADH-ubiquinone oxidoreductase chain 2: “Activity optimized complex I (closed form)”. Electron microscopy, 8 ligands (SF4, 3PE, PC1), 20 pockets (best druggability 0.90). MolNFT v1 #176268 on GenesisL1: 3D structure, binding sites…
- PDB
- 7DGZ
- Type
- protein
- Length
- 7,992 residues
- Chains
- 45
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH-ubiquinone oxidoreductase chain 2; NADH-ubiquinone oxidoreductase chain 3…
- EC
- 7.1.1.2
- UniProt
- P03892, P03898, P03910, P03902, P03924, P25708, P04394, P15690, P17694, P23709, P42026, P42028, P25712, Q02375, Q02379, P23934, Q02377, Q02370, Q02371, P23935, Q02366, Q05752, P42029, P34943, P34942, Q8HXG6, O97725, Q95KV7, P52505, Q02378, Q02374, Q02365, P48305, Q02380, Q02367, Q02368, Q02369, Q8HXG5, Q02376, Q02827, P03887, P03920, Q02373, Q02372
- Ligands
- SF4, 3PE, PC1, CDL, FES, FMN, NAP, ZN
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · 45 distinct chains · 35% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 2 | NADH-ubiquinone oxidoreductase chain 2 (EC 7.1.1.2) | protein | 344 | 46% helix, 1% strand | P03892 |
| 3 | NADH-ubiquinone oxidoreductase chain 3 (EC 7.1.1.2) | protein | 112 | 43% helix, 0% strand | P03898 |
| 4 | NADH-ubiquinone oxidoreductase chain 4 (EC 7.1.1.2) | protein | 458 | 49% helix, 0% strand | P03910 |
| 5 | NADH-ubiquinone oxidoreductase chain 4L (EC 7.1.1.2) | protein | 96 | 57% helix, 0% strand | P03902 |
| 7 | NADH-ubiquinone oxidoreductase chain 6 (EC 7.1.1.2) | protein | 172 | 54% helix, 0% strand | P03924 |
| 8 | NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (EC 7.1.1.2) | protein | 427 | 28% helix, 9% strand | P25708 |
| 9 | NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial (EC 7.1.1.2) | protein | 207 | 31% helix, 7% strand | P04394 |
| A | NADH-ubiquinone oxidoreductase 75 kda subunit, mitochondrial (EC 7.1.1.2) | protein | 688 | 19% helix, 13% strand | P15690 |
| B | NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial (EC 7.1.1.2) | protein | 430 | 30% helix, 7% strand | P17694 |
| C | NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial (EC 7.1.1.2) | protein | 208 | 17% helix, 18% strand | P23709 |
| D | NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial (EC 7.1.1.2) | protein | 152 | 25% helix, 9% strand | P42026 |
| E | NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial (EC 7.1.1.2) | protein | 176 | 19% helix, 13% strand | P42028 |
| F | NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial | protein | 28 | 0% helix, 0% strand | P25712 |
| G | NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial | protein | 123 | 7% helix, 9% strand | Q02375 |
| H | NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 | protein | 96 | 39% helix, 0% strand | Q02379 |
| I | NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial | protein | 71 | 0% helix, 14% strand | P23934 |
| J | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 | protein | 69 | 61% helix, 0% strand | Q02377 |
| K | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 | protein | 84 | 23% helix, 19% strand | Q02370 |
| L | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 | protein | 80 | 19% helix, 0% strand | Q02371 |
| N | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 | protein | 111 | 49% helix, 0% strand | P23935 |
| O | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 | protein | 114 | 51% helix, 0% strand | Q02366 |
| P | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 | protein | 90 | 4% helix, 3% strand | Q05752 |
| Q | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 | protein | 168 | 29% helix, 0% strand | P42029 |
| R | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial | protein | 319 | 17% helix, 8% strand | P34943 |
| S | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial | protein | 319 | 27% helix, 3% strand | P34942 |
| T | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 | protein | 138 | 60% helix, 0% strand | Q8HXG6 |
| U | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 | protein | 132 | 14% helix, 0% strand | O97725 |
| V | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 | protein | 138 | 43% helix, 0% strand | Q95KV7 |
| W | Acyl carrier protein, mitochondrial | protein | 86 | 41% helix, 0% strand | P52505 |
| X | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 | protein | 49 | 20% helix, 0% strand | Q02378 |
| Y | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial | protein | 57 | 30% helix, 0% strand | Q02374 |
| Z | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 | protein | 74 | 19% helix, 0% strand | Q02365 |
| a | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 | protein | 114 | 42% helix, 0% strand | P48305 |
| b | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial | protein | 139 | 33% helix, 1% strand | Q02380 |
| c | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 | protein | 90 | 32% helix, 0% strand | Q02367 |
| d | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 | protein | 107 | 39% helix, 0% strand | Q02368 |
| f | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 | protein | 167 | 33% helix, 0% strand | Q02369 |
| h | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial | protein | 91 | 43% helix, 0% strand | Q8HXG5 |
| i | NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial | protein | 38 | 71% helix, 0% strand | Q02376 |
| j | NADH dehydrogenase [ubiquinone] 1 subunit C2 | protein | 113 | 54% helix, 1% strand | Q02827 |
| 1 | NADH-ubiquinone oxidoreductase chain 1 (EC 7.1.1.2) | protein | 317 | 53% helix, 0% strand | P03887 |
| 6 | NADH-ubiquinone oxidoreductase chain 5 (EC 7.1.1.2) | protein | 606 | 59% helix, 1% strand | P03920 |
| g | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 | protein | 173 | 46% helix, 1% strand | Q02373 |
| e | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial | protein | 141 | 10% helix, 0% strand | Q02372 |
| M | Acyl carrier protein, mitochondrial | protein | 80 | 43% helix, 0% strand | P52505 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 6 copies · chains 8, A, B, D, E
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 4 copies · chains 2, 4, j, T, B, E, L, V, 1, 3, 7, J
- PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 4 copies · chains 3, L, 1, 2, 4, Q, j, S, H
- CDL · Cardiolipin · ligand · 2 copies · chains 4, b, h, 6, J, P, U
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains 8, 9, A
- FMN · Flavin mononucleotide · ligand · chains 8
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · chains D, R
- ZN · Zinc ion · metal · chains I
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 | 1045 | 0.90 | 0.91 | 147 | empty |
| 2 | 927 | 0.89 | 0.91 | 105 | 3PE |
| 3 | 906 | 0.88 | 0.90 | 129 | empty |
| 4 | 882 | 0.88 | 0.90 | 123 | empty |
| 5 | 560 | 0.87 | 0.93 | 80 | empty |
Interfaces
189 interfaces between chains.
- 3–1 · 2757 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 2706 Ų buried · 19 hydrogen bonds · protein-protein
- 8–9 · 2678 Ų buried · 21 hydrogen bonds · protein-protein
- 5–7 · 2419 Ų buried · 3 hydrogen bonds · protein-protein
- B–E · 2256 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 7DGZ · Activity optimized complex I (closed form) · the same entry in another collection · chain D against D, 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 P03892
- Every structure of UniProt P03898
- Every structure of UniProt P03910
- Every structure of UniProt P03902
- Every structure of UniProt P03924
- Every structure of UniProt P25708
- Every structure of UniProt P04394
- Every structure of UniProt P15690
- Every structure of UniProt P17694
- Every structure of UniProt P23709
- Every structure of UniProt P42026
- Every structure of UniProt P42028
- Every structure of UniProt P25712
- Every structure of UniProt Q02375
- Every structure of UniProt Q02379
- Every structure of UniProt P23934
- Every structure of UniProt Q02377
- Every structure of UniProt Q02370
- Every structure of UniProt Q02371
- Every structure of UniProt P23935
- Every structure of UniProt Q02366
- Every structure of UniProt Q05752
- Every structure of UniProt P42029
- Every structure of UniProt P34943
- Every structure of UniProt P34942
- Every structure of UniProt Q8HXG6
- Every structure of UniProt O97725
- Every structure of UniProt Q95KV7
- Every structure of UniProt P52505
- Every structure of UniProt Q02378
- Every structure of UniProt Q02374
- Every structure of UniProt Q02365
- Every structure of UniProt P48305
- Every structure of UniProt Q02380
- Every structure of UniProt Q02367
- Every structure of UniProt Q02368
- Every structure of UniProt Q02369
- Every structure of UniProt Q8HXG5
- Every structure of UniProt Q02376
- Every structure of UniProt Q02827
- Every structure of UniProt P03887
- Every structure of UniProt P03920
- Every structure of UniProt Q02373
- Every structure of UniProt Q02372
- Elsewhere: RCSB PDB 7DGZ · PDBe 7DGZ · UniProt P03892 · UniProt P03898 · UniProt P03910 · UniProt P03902 · UniProt P03924 · UniProt P25708 · UniProt P04394 · UniProt P15690 · UniProt P17694 · UniProt P23709 · UniProt P42026 · UniProt P42028 · UniProt P25712 · UniProt Q02375 · UniProt Q02379 · UniProt P23934 · UniProt Q02377 · UniProt Q02370 · UniProt Q02371 · UniProt P23935 · UniProt Q02366 · UniProt Q05752 · UniProt P42029 · UniProt P34943 · UniProt P34942 · UniProt Q8HXG6 · UniProt O97725 · UniProt Q95KV7 · UniProt P52505 · UniProt Q02378 · UniProt Q02374 · UniProt Q02365 · UniProt P48305 · UniProt Q02380 · UniProt Q02367 · UniProt Q02368 · UniProt Q02369 · UniProt Q8HXG5 · UniProt Q02376 · UniProt Q02827 · UniProt P03887 · UniProt P03920 · UniProt Q02373 · UniProt Q02372
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