MolNFT v1 · #125608 · protein
Structure of mammalian respiratory complex I, CLASS3.
5LDX · NADH-ubiquinone oxidoreductase chain 3: “Structure of mammalian respiratory complex I, CLASS3.”. Electron microscopy, 5 ligands (SF4, FES, FMN), 20 pockets (best druggability 0.88). MolNFT v1 #125608 on GenesisL1: 3D structure…
- PDB
- 5LDX
- Type
- protein
- Length
- 7,791 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, P15690, P03887, P42028, P03924, P03902, P03920, P03910, P03892, P34942, P23934, Q02370, P52505, P23935, Q02366, P42029, Q8HXG6, Q95KV7, Q02377, Q02371, Q02376, Q02827, Q02379, Q02378, Q8HXG5, Q02380, Q02367, P48305, Q02369, Q02368, Q02373, O97725
- Ligands
- SF4, FES, FMN, NAP, ZN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 45 distinct chains · 43% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) | protein | 88 | 74% 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 | 206 | 12% helix, 18% strand | P23709 |
| D | NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial (EC 1.6.5.3, 1.6.99.3) | protein | 416 | 41% helix, 8% strand | P17694 |
| E | NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial (EC 1.6.5.3, 1.6.99.3) | protein | 186 | 32% helix, 9% strand | P04394 |
| F | NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (EC 1.6.5.3, 1.6.99.3) | protein | 425 | 38% helix, 10% strand | P25708 |
| G | NADH-ubiquinone oxidoreductase 75 kda subunit, MITOCHONDRIAL,NADH-ubiquinone oxidoreductase 75 kda subunit, MITOCHONDRIAL,NADH-ubiquinone oxidoreductase 75 kda subunit, MITOCHONDRIAL,NADH-ubiquinone oxidoreductase 75 kda subunit, mitochondrial (EC 1.6.5.3, 1.6.99.3) | protein | 685 | 23% helix, 8% strand | P15690 |
| H | NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) | protein | 296 | 62% 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, 7% 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 | 72% helix, 0% strand | P03902 |
| L | NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) | protein | 604 | 63% helix, 1% 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 | 64% helix, 1% strand | P03892 |
| O | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, MITOCHONDRIAL,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, MITOCHONDRIAL,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial | protein | 314 | 39% helix, 6% strand | P34942 |
| P | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, NDUFA9 | protein | 283 | 27% helix, 10% strand | — |
| Q | NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, NDUFS4 | protein | 113 | 9% helix, 15% strand | — |
| R | NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, MITOCHONDRIAL,NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, MITOCHONDRIAL,NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial | protein | 89 | 6% helix, 21% strand | P23934 |
| S | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 | protein | 80 | 36% helix, 10% strand | Q02370 |
| T | Acyl carrier protein, mitochondrial | protein | 75 | 49% helix, 0% strand | P52505 |
| U | Acyl carrier protein, mitochondrial | protein | 85 | 42% helix, 0% strand | P52505 |
| V | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 | protein | 106 | 54% helix, 0% strand | P23935 |
| W | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 | protein | 111 | 47% helix, 0% strand | Q02366 |
| X | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 | protein | 164 | 34% helix, 0% strand | P42029 |
| Y | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 | protein | 138 | 64% helix, 0% strand | Q8HXG6 |
| Z | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 | protein | 138 | 51% helix, 0% strand | Q95KV7 |
| a | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 | protein | 64 | 59% helix, 0% strand | Q02377 |
| b | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 | protein | 80 | 44% helix, 0% strand | Q02371 |
| c | NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial | protein | 46 | 63% helix, 0% strand | Q02376 |
| d | NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2 | protein | 114 | 50% helix, 0% strand | Q02827 |
| e | NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 | protein | 89 | 46% helix, 0% strand | Q02379 |
| f | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 | protein | 54 | 44% helix, 0% strand | Q02378 |
| g | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial | protein | 97 | 35% helix, 0% strand | Q8HXG5 |
| h | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, MITOCHONDRIAL,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, MITOCHONDRIAL,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial | protein | 134 | 53% helix, 0% strand | Q02380 |
| i | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 | protein | 106 | 44% helix, 2% strand | Q02367 |
| j | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, NDUFB2 | protein | 52 | 35% helix, 0% strand | — |
| k | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3, NDUFB3 | protein | 74 | 38% helix, 0% strand | — |
| l | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, NDUFB8 | protein | 118 | 20% helix, 0% strand | — |
| m | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 | protein | 118 | 53% helix, 0% strand | P48305 |
| n | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 | protein | 166 | 45% helix, 0% strand | Q02369 |
| o | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 | protein | 58 | 76% 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,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,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 | 58% helix, 0% strand | Q02373 |
| q | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 | protein | 138 | 13% helix, 1% strand | O97725 |
| r | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7, NDUFA7 | protein | 87 | 8% helix, 1% strand | — |
| s | NADH dehydrogenase [ubiquinone] flavoprotein 3, NDUFV3 | protein | 35 | 23% helix, 0% strand | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 6 copies · chains B, D, F, G, I
- 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 | 652 | 0.88 | 0.92 | 131 | empty |
| 2 | 922 | 0.88 | 0.90 | 166 | empty |
| 3 | 998 | 0.87 | 0.89 | 156 | empty |
| 4 | 915 | 0.86 | 0.88 | 132 | empty |
| 5 | 693 | 0.85 | 0.89 | 102 | empty |
Interfaces
184 interfaces between chains.
- J–K · 3074 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 2900 Ų buried · 30 hydrogen bonds · protein-protein
- L–M · 2594 Ų buried · 12 hydrogen bonds · protein-protein
- A–H · 2403 Ų buried · 1 hydrogen bond · protein-protein
- D–I · 2394 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide (disulfide).
Compared structures
- 5LDX · Structure of mammalian respiratory Complex I, class3. · 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 P15690
- 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 P23934
- Every structure of UniProt Q02370
- Every structure of UniProt P52505
- Every structure of UniProt P23935
- Every structure of UniProt Q02366
- Every structure of UniProt P42029
- Every structure of UniProt Q8HXG6
- Every structure of UniProt Q95KV7
- Every structure of UniProt Q02377
- Every structure of UniProt Q02371
- Every structure of UniProt Q02376
- Every structure of UniProt Q02827
- Every structure of UniProt Q02379
- Every structure of UniProt Q02378
- Every structure of UniProt Q8HXG5
- Every structure of UniProt Q02380
- Every structure of UniProt Q02367
- Every structure of UniProt P48305
- Every structure of UniProt Q02369
- Every structure of UniProt Q02368
- Every structure of UniProt Q02373
- Every structure of UniProt O97725
- Elsewhere: RCSB PDB 5LDX · PDBe 5LDX · UniProt P03898 · UniProt P42026 · UniProt P23709 · UniProt P17694 · UniProt P04394 · UniProt P25708 · UniProt P15690 · UniProt P03887 · UniProt P42028 · UniProt P03924 · UniProt P03902 · UniProt P03920 · UniProt P03910 · UniProt P03892 · UniProt P34942 · UniProt P23934 · UniProt Q02370 · UniProt P52505 · UniProt P23935 · UniProt Q02366 · UniProt P42029 · UniProt Q8HXG6 · UniProt Q95KV7 · UniProt Q02377 · UniProt Q02371 · UniProt Q02376 · UniProt Q02827 · UniProt Q02379 · UniProt Q02378 · UniProt Q8HXG5 · UniProt Q02380 · UniProt Q02367 · UniProt P48305 · UniProt Q02369 · UniProt Q02368 · UniProt Q02373 · UniProt O97725
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