MolNFT v1 · #128853 · protein
Mitochondrial complex I in the deactive state
5O31 · NADH-ubiquinone oxidoreductase chain 3: “Mitochondrial complex I in the deactive state”. Electron microscopy, 5 ligands (SF4, FES, FMN), 20 pockets (best druggability 0.88). MolNFT v1 #128853 on GenesisL1: 3D structure, binding…
- PDB
- 5O31
- Type
- protein
- Length
- 7,811 residues
- Chains
- 45
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH-ubiquinone oxidoreductase chain 3; NADH dehydrogenase [ubiquinone] iron-sulfur…
- EC
- 1.6.5.3, 1.6.99.3
- UniProt
- P03898, P42026, P23709, P17694, P04394, P25708, P03887, P42028, P03924, P03902, P03920, P03910, P03892, P34942, Q02370, P52505, P23935, Q02366, Q8HXG6, Q02377, Q02371, Q02376, Q02379, Q02378, Q8HXG5, Q02367, Q02368, Q02373, O97725, P15690, P25712, Q02375, P23934, Q05752, Q02380, Q02827, P42029, P48305, Q02369, Q95KV7
- Ligands
- SF4, FES, FMN, NAP, ZN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 45 distinct chains · 44% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) | protein | 88 | 72% helix, 0% strand | P03898 |
| B | NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial (EC 1.6.5.3, 1.6.99.3) | protein | 147 | 34% helix, 11% strand | P42026 |
| C | NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial (EC 1.6.5.3, 1.6.99.3) | protein | 204 | 12% helix, 20% strand | P23709 |
| D | NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial (EC 1.6.5.3, 1.6.99.3) | protein | 416 | 41% helix, 9% strand | P17694 |
| E | NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial (EC 1.6.5.3, 1.6.99.3) | protein | 186 | 38% helix, 11% strand | P04394 |
| F | NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (EC 1.6.5.3, 1.6.99.3) | protein | 425 | 40% helix, 9% strand | P25708 |
| H | NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) | protein | 296 | 60% helix, 0% strand | P03887 |
| I | NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial (EC 1.6.5.3, 1.6.99.3) | protein | 176 | 31% helix, 15% strand | P42028 |
| J | NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) | protein | 171 | 58% helix, 0% strand | P03924 |
| K | NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) | protein | 95 | 73% helix, 0% strand | P03902 |
| L | NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) | protein | 604 | 64% helix, 2% strand | P03920 |
| M | NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) | protein | 457 | 60% helix, 0% strand | P03910 |
| N | NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) | protein | 344 | 63% helix, 1% strand | P03892 |
| O | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial | protein | 314 | 41% helix, 7% strand | P34942 |
| P | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9 | protein | 283 | 29% helix, 11% strand | — |
| S | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 | protein | 80 | 34% helix, 15% strand | Q02370 |
| T | Acyl carrier protein, mitochondrial | protein | 75 | 57% helix, 0% strand | P52505 |
| U | Acyl carrier protein, mitochondrial | protein | 85 | 52% helix, 0% strand | P52505 |
| V | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 | protein | 106 | 52% helix, 0% strand | P23935 |
| W | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 | protein | 111 | 47% helix, 0% strand | Q02366 |
| Y | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 | protein | 138 | 61% helix, 0% strand | Q8HXG6 |
| a | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 | protein | 64 | 58% helix, 0% strand | Q02377 |
| b | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 | protein | 80 | 45% helix, 0% strand | Q02371 |
| c | NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial | protein | 46 | 65% helix, 0% strand | Q02376 |
| e | NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 | protein | 89 | 43% helix, 0% strand | Q02379 |
| f | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 | protein | 54 | 35% helix, 0% strand | Q02378 |
| g | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial | protein | 97 | 42% helix, 0% strand | Q8HXG5 |
| i | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 | protein | 106 | 43% helix, 2% strand | Q02367 |
| j | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2 | protein | 52 | 33% helix, 0% strand | — |
| k | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 | protein | 74 | 26% helix, 0% strand | — |
| l | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 | protein | 118 | 19% helix, 0% strand | — |
| o | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 | protein | 58 | 72% helix, 0% strand | Q02368 |
| p | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 | protein | 169 | 56% helix, 1% strand | Q02373 |
| q | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 | protein | 138 | 20% helix, 3% strand | O97725 |
| G | NADH-ubiquinone oxidoreductase 75 kda subunit, mitochondrial (EC 1.6.5.3, 1.6.99.3) | protein | 688 | 26% helix, 15% strand | P15690 |
| s | NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial | protein | 41 | 17% helix, 0% strand | P25712 |
| Q | NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial | protein | 123 | 12% helix, 13% strand | Q02375 |
| R | NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial | protein | 93 | 11% helix, 18% strand | P23934 |
| r | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 | protein | 88 | 11% helix, 2% strand | Q05752 |
| h | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial | protein | 134 | 43% helix, 1% strand | Q02380 |
| d | NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2 | protein | 113 | 48% helix, 0% strand | Q02827 |
| X | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 | protein | 164 | 37% helix, 0% strand | P42029 |
| m | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 | protein | 118 | 52% helix, 1% strand | P48305 |
| n | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 | protein | 166 | 46% helix, 0% strand | Q02369 |
| Z | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 | protein | 137 | 50% helix, 0% strand | Q95KV7 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 6 copies · chains B, D, F, I, G
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains E, F, G
- FMN · Flavin mononucleotide · ligand · chains F
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · chains P
- ZN · Zinc ion · metal · chains R
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 | 710 | 0.88 | 0.92 | 117 | empty |
| 2 | 1180 | 0.87 | 0.88 | 178 | empty |
| 3 | 1161 | 0.87 | 0.88 | 145 | empty |
| 4 | 922 | 0.87 | 0.89 | 124 | empty |
| 5 | 655 | 0.87 | 0.91 | 106 | empty |
Interfaces
182 interfaces between chains.
- J–K · 3013 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 2792 Ų buried · 28 hydrogen bonds · protein-protein
- L–M · 2517 Ų buried · 4 hydrogen bonds · protein-protein
- D–I · 2426 Ų buried · 34 hydrogen bonds · protein-protein
- A–H · 2405 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5O31 · Mitochondrial complex I in the deactive state · the same entry in another collection · chain K against K, 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 P03898
- Every structure of UniProt P42026
- Every structure of UniProt P23709
- Every structure of UniProt P17694
- Every structure of UniProt P04394
- Every structure of UniProt P25708
- Every structure of UniProt P03887
- Every structure of UniProt P42028
- Every structure of UniProt P03924
- Every structure of UniProt P03902
- Every structure of UniProt P03920
- Every structure of UniProt P03910
- Every structure of UniProt P03892
- Every structure of UniProt P34942
- Every structure of UniProt Q02370
- Every structure of UniProt P52505
- Every structure of UniProt P23935
- Every structure of UniProt Q02366
- Every structure of UniProt Q8HXG6
- Every structure of UniProt Q02377
- Every structure of UniProt Q02371
- Every structure of UniProt Q02376
- Every structure of UniProt Q02379
- Every structure of UniProt Q02378
- Every structure of UniProt Q8HXG5
- Every structure of UniProt Q02367
- Every structure of UniProt Q02368
- Every structure of UniProt Q02373
- Every structure of UniProt O97725
- Every structure of UniProt P15690
- Every structure of UniProt P25712
- Every structure of UniProt Q02375
- Every structure of UniProt P23934
- Every structure of UniProt Q05752
- Every structure of UniProt Q02380
- Every structure of UniProt Q02827
- Every structure of UniProt P42029
- Every structure of UniProt P48305
- Every structure of UniProt Q02369
- Every structure of UniProt Q95KV7
- Elsewhere: RCSB PDB 5O31 · PDBe 5O31 · UniProt P03898 · UniProt P42026 · UniProt P23709 · UniProt P17694 · UniProt P04394 · UniProt P25708 · UniProt P03887 · UniProt P42028 · UniProt P03924 · UniProt P03902 · UniProt P03920 · UniProt P03910 · UniProt P03892 · UniProt P34942 · UniProt Q02370 · UniProt P52505 · UniProt P23935 · UniProt Q02366 · UniProt Q8HXG6 · UniProt Q02377 · UniProt Q02371 · UniProt Q02376 · UniProt Q02379 · UniProt Q02378 · UniProt Q8HXG5 · UniProt Q02367 · UniProt Q02368 · UniProt Q02373 · UniProt O97725 · UniProt P15690 · UniProt P25712 · UniProt Q02375 · UniProt P23934 · UniProt Q05752 · UniProt Q02380 · UniProt Q02827 · UniProt P42029 · UniProt P48305 · UniProt Q02369 · UniProt Q95KV7
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