MolNFT v1 · #139886 · protein
Cryo-EM structure of human respiratory complex I matrix arm
5XTB · NADH dehydrogenase [ubiquinone] flavoprotein 1…: “Cryo-EM structure of human respiratory complex I matrix arm”. Electron microscopy, 5 ligands (SF4, FES, FMN), 20 pockets (best druggability 0.89). MolNFT v1 #139886 on GenesisL1: 3D…
- PDB
- 5XTB
- Type
- protein
- Length
- 3,491 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial; NADH dehydrogenase…
- EC
- 1.6.5.3, 1.6.99.3
- UniProt
- P49821, O00217, O75251, P56556, O43678, O14561, Q16718, O95182, Q16795, P56181, O43181, P28331, Q9UI09, P19404, O75489, O75306, O75380, Q9P0J0
- Ligands
- SF4, FES, FMN, 8Q1, NDP
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 18 distinct chains · 36% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (EC 1.6.5.3, 1.6.99.3) | protein | 431 | 43% helix, 12% strand | P49821 |
| B | NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial (EC 1.6.5.3, 1.6.99.3) | protein | 176 | 36% helix, 14% strand | O00217 |
| C | NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial (EC 1.6.5.3, 1.6.99.3) | protein | 156 | 46% helix, 6% strand | O75251 |
| E | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 | protein | 113 | 58% helix, 0% strand | P56556 |
| F | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 | protein | 83 | 37% helix, 19% strand | O43678 |
| G | Acyl carrier protein, mitochondrial | protein | 85 | 53% helix, 0% strand | O14561 |
| H | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 | protein | 112 | 54% helix, 0% strand | Q16718 |
| I | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 | protein | 95 | 19% helix, 4% strand | O95182 |
| J | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial | protein | 337 | 41% helix, 11% strand | Q16795 |
| K | NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial | protein | 33 | 36% helix, 0% strand | P56181 |
| L | NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial | protein | 118 | 20% helix, 18% strand | O43181 |
| M | NADH-ubiquinone oxidoreductase 75 kda subunit, mitochondrial (EC 1.6.5.3, 1.6.99.3) | protein | 687 | 30% helix, 10% strand | P28331 |
| N | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 | protein | 143 | 22% helix, 3% strand | Q9UI09 |
| O | NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial (EC 1.6.5.3, 1.6.99.3) | protein | 212 | 35% helix, 2% strand | P19404 |
| P | NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial (EC 1.6.5.3, 1.6.99.3) | protein | 208 | 19% helix, 20% strand | O75489 |
| Q | NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial (EC 1.6.5.3, 1.6.99.3) | protein | 385 | 48% helix, 12% strand | O75306 |
| T | NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial | protein | 95 | 14% helix, 13% strand | O75380 |
| W | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 | protein | 22 | 0% helix, 5% strand | Q9P0J0 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 6 copies · chains A, B, C, Q, M
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains M, O
- FMN · Flavin mononucleotide · ligand · chains A
- 8Q1 · S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy) butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate · ligand · chains E, G
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains J
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 | 1194 | 0.89 | 0.91 | 150 | empty |
| 2 | 1113 | 0.87 | 0.88 | 120 | 8Q1 |
| 3 | 1079 | 0.83 | 0.84 | 105 | empty |
| 4 | 619 | 0.83 | 0.88 | 76 | empty |
| 5 | 825 | 0.83 | 0.85 | 68 | NDP |
Interfaces
62 interfaces between chains.
- A–O · 3112 Ų buried · 32 hydrogen bonds · protein-protein
- P–Q · 2551 Ų buried · 22 hydrogen bonds · protein-protein
- B–N · 2117 Ų buried · 21 hydrogen bonds · protein-protein
- B–Q · 2117 Ų buried · 24 hydrogen bonds · protein-protein
- L–M · 1921 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5XTB · Cryo-EM structure of human respiratory complex I matrix arm · the same entry in another collection · chain L against L, 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 P49821
- Every structure of UniProt O00217
- Every structure of UniProt O75251
- Every structure of UniProt P56556
- Every structure of UniProt O43678
- Every structure of UniProt O14561
- Every structure of UniProt Q16718
- Every structure of UniProt O95182
- Every structure of UniProt Q16795
- Every structure of UniProt P56181
- Every structure of UniProt O43181
- Every structure of UniProt P28331
- Every structure of UniProt Q9UI09
- Every structure of UniProt P19404
- Every structure of UniProt O75489
- Every structure of UniProt O75306
- Every structure of UniProt O75380
- Every structure of UniProt Q9P0J0
- Elsewhere: RCSB PDB 5XTB · PDBe 5XTB · UniProt P49821 · UniProt O00217 · UniProt O75251 · UniProt P56556 · UniProt O43678 · UniProt O14561 · UniProt Q16718 · UniProt O95182 · UniProt Q16795 · UniProt P56181 · UniProt O43181 · UniProt P28331 · UniProt Q9UI09 · UniProt P19404 · UniProt O75489 · UniProt O75306 · UniProt O75380 · UniProt Q9P0J0
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