MolNFT v1 · #173160 · protein
Cryo-EM structure of arabidopsis thaliana complex-I (membrane core)
7AQQ · NADH-ubiquinone oxidoreductase chain 3: “Cryo-EM structure of arabidopsis thaliana complex-I (membrane core)”. Electron microscopy, 9 ligands (PTY, UQ9, LMN), 20 pockets (best druggability 0.86). MolNFT v1 #173160 on GenesisL1: 3D…
- PDB
- 7AQQ
- Type
- protein
- Length
- 2,917 residues
- Chains
- 21
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH-ubiquinone oxidoreductase chain 3; NADH-ubiquinone oxidoreductase chain 1…
- EC
- 7.1.1.2, 4.2.1.-
- UniProt
- P92533, B5TM92, A0A2P2CLG1, A0A2P2CLH7, B5TM94, B5TM93, O05000, A0A384LA38, Q8LGE7, Q8RWA7, Q9C9Z5, Q9ZPY5, Q94AL6, Q9LZI6, Q84W12, A0A178W1I8, Q9ZUX4, Q9SMN1, Q9C6B3, Q9FWR5
- Ligands
- PTY, UQ9, LMN, PC7, PGT, PSF, T7X, FE, ZN
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 21 distinct chains · 57% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NADH-ubiquinone oxidoreductase chain 3 (EC 7.1.1.2) | protein | 92 | 74% helix, 0% strand | P92533 |
| H | NADH-ubiquinone oxidoreductase chain 1 (EC 7.1.1.2) | protein | 311 | 67% helix, 0% strand | B5TM92 |
| J | NADH-ubiquinone oxidoreductase chain 6 (EC 7.1.1.2) | protein | 147 | 66% helix, 0% strand | A0A2P2CLG1 |
| K | NADH dehydrogenase subunit 4L | protein | 90 | 84% helix, 0% strand | A0A2P2CLH7 |
| L | NADH-ubiquinone oxidoreductase chain 5 (EC 7.1.1.2) | protein | 26 | 62% helix, 0% strand | B5TM94 |
| M | NADH-ubiquinone oxidoreductase chain 4 (EC 7.1.1.2) | protein | 262 | 68% helix, 6% strand | B5TM93 |
| N | NADH-ubiquinone oxidoreductase chain 2 (EC 7.1.1.2) | protein | 488 | 74% helix, 1% strand | O05000 |
| O | AT3G07480.1 | protein | 122 | 22% helix, 23% strand | A0A384LA38 |
| X | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B | protein | 97 | 74% helix, 0% strand | Q8LGE7 |
| Z | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-a | protein | 98 | 63% helix, 0% strand | Q8RWA7 |
| a | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 | protein | 58 | 78% helix, 0% strand | Q9C9Z5 |
| b | AT2G46540/F11C10.23 | protein | 40 | 85% helix, 0% strand | Q9ZPY5 |
| d | Excitatory amino acid transporter | protein | 75 | 84% helix, 0% strand | Q94AL6 |
| e | NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-B | protein | 65 | 63% helix, 3% strand | Q9LZI6 |
| f | AT4G16450 | protein | 101 | 62% helix, 0% strand | Q84W12 |
| i | P1 | protein | 70 | 53% helix, 0% strand | A0A178W1I8 |
| u | Unknown | protein | 30 | 80% helix, 0% strand | — |
| v | Uncharacterized protein AT2G27730, mitochondrial | protein | 30 | 77% helix, 0% strand | Q9ZUX4 |
| x | Gamma carbonic anhydrase-like 2, mitochondrial | protein | 214 | 15% helix, 32% strand | Q9SMN1 |
| y | Gamma carbonic anhydrase 2, mitochondrial (EC 4.2.1.-) | protein | 268 | 28% helix, 20% strand | Q9C6B3 |
| z | Gamma carbonic anhydrase 1, mitochondrial (EC 4.2.1.-) | protein | 233 | 27% helix, 26% strand | Q9FWR5 |
Ligands and binding sites
- PTY · Phosphatidylethanolamine · ligand · 2 copies · chains H, Z, b, N, d
- UQ9 · Ubiquinone-9 · ligand · chains H
- LMN · Lauryl Maltose Neopentyl Glycol · ligand · chains M, N, d
- PC7 · (7S)-4-hydroxy-N,N,N-trimethyl-9-oxo-7-[(palmitoyloxy) methyl]-3,5,8-trioxa-4-phosphahexacosan-1-aminium 4-oxide · ligand · chains N, f, v
- PGT · (1S)-2-{[{[(2R)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate · ligand · chains N, f, y
- PSF · 1,2-dicaproyl-sn-phosphatidyl-L-serine · ligand · chains N, d, x, z
- T7X · Phosphatidylinositol · ligand · chains f, v, y, z
- FE · Fe (III) ion · metal · chains O
- ZN · Zinc ion · metal · chains y, z
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 | 1072 | 0.86 | 0.87 | 100 | empty |
| 2 | 1090 | 0.83 | 0.84 | 72 | empty |
| 3 | 788 | 0.80 | 0.83 | 65 | PTY |
| 4 | 641 | 0.80 | 0.85 | 64 | empty |
| 5 | 871 | 0.78 | 0.81 | 74 | empty |
Interfaces
69 interfaces between chains.
- x–z · 2665 Ų buried · 21 hydrogen bonds · protein-protein
- A–H · 2603 Ų buried · 3 hydrogen bonds · protein-protein
- y–z · 2562 Ų buried · 25 hydrogen bonds · protein-protein
- x–y · 2562 Ų buried · 34 hydrogen bonds · protein-protein
- J–K · 2521 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7AQQ · Cryo-EM structure of Arabidopsis thaliana Complex-I (membrane core) · the same entry in another collection · chain e against e, 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 P92533
- Every structure of UniProt B5TM92
- Every structure of UniProt A0A2P2CLG1
- Every structure of UniProt A0A2P2CLH7
- Every structure of UniProt B5TM94
- Every structure of UniProt B5TM93
- Every structure of UniProt O05000
- Every structure of UniProt A0A384LA38
- Every structure of UniProt Q8LGE7
- Every structure of UniProt Q8RWA7
- Every structure of UniProt Q9C9Z5
- Every structure of UniProt Q9ZPY5
- Every structure of UniProt Q94AL6
- Every structure of UniProt Q9LZI6
- Every structure of UniProt Q84W12
- Every structure of UniProt A0A178W1I8
- Every structure of UniProt Q9ZUX4
- Every structure of UniProt Q9SMN1
- Every structure of UniProt Q9C6B3
- Every structure of UniProt Q9FWR5
- Elsewhere: RCSB PDB 7AQQ · PDBe 7AQQ · UniProt P92533 · UniProt B5TM92 · UniProt A0A2P2CLG1 · UniProt A0A2P2CLH7 · UniProt B5TM94 · UniProt B5TM93 · UniProt O05000 · UniProt A0A384LA38 · UniProt Q8LGE7 · UniProt Q8RWA7 · UniProt Q9C9Z5 · UniProt Q9ZPY5 · UniProt Q94AL6 · UniProt Q9LZI6 · UniProt Q84W12 · UniProt A0A178W1I8 · UniProt Q9ZUX4 · UniProt Q9SMN1 · UniProt Q9C6B3 · UniProt Q9FWR5
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