Research workbench
Matrix arm of deactive state ci from rotenone-NADH dataset
Analyse Matrix arm of deactive state ci from rotenone-NADH dataset in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VWJ
- Type
- protein
- Length
- 3,488 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial; NADH dehydrogenase…
- EC
- 7.1.1.2
- UniProt
- F1RVN1, A0A287BDC0, I3LK43, A0A480VKQ8, F1RGE3, D0G781, A0A5G2RN85, A0A4X1VLA2, A0A480QJC4, A0A4X1TFI3, G8IFA6, F1SHD7, F1SQP4, A0A287BG40, A0A286ZNN4, A0A480JYS1, F1S031, F1S6Q1
- Ligands
- SF4, FES, FMN, NAI, PEE, PLX, 8Q1, CDL, NDP, MG, ZN
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · 18 distinct chains · 38% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (EC 7.1.1.2) | protein | 431 | 47% helix, 14% strand | F1RVN1 |
| B | NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial | protein | 176 | 37% helix, 17% strand | A0A287BDC0 |
| C | NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial | protein | 156 | 51% helix, 13% strand | I3LK43 |
| E | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 | protein | 115 | 60% helix, 0% strand | A0A480VKQ8 |
| F | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 | protein | 86 | 42% helix, 30% strand | F1RGE3 |
| G | Acyl carrier protein, mitochondrial | protein | 88 | 50% helix, 0% strand | D0G781 |
| H | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 | protein | 112 | 56% helix, 0% strand | A0A5G2RN85 |
| I | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 | protein | 97 | 18% helix, 4% strand | A0A4X1VLA2 |
| J | NADH dehydrogenase ubiquinone 1 alpha subcomplex subunit 9, mitochondrial | protein | 297 | 41% helix, 15% strand | A0A480QJC4 |
| K | NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial | protein | 42 | 40% helix, 0% strand | A0A4X1TFI3 |
| L | NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial | protein | 125 | 18% helix, 18% strand | G8IFA6 |
| M | NADH-ubiquinone oxidoreductase 75 kda subunit, mitochondrial | protein | 690 | 33% helix, 17% strand | F1SHD7 |
| N | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 | protein | 144 | 24% helix, 11% strand | F1SQP4 |
| O | NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial | protein | 217 | 37% helix, 12% strand | A0A287BG40 |
| P | NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial | protein | 208 | 22% helix, 27% strand | A0A286ZNN4 |
| Q | NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial | protein | 379 | 51% helix, 14% strand | A0A480JYS1 |
| T | NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial | protein | 96 | 16% helix, 20% strand | F1S031 |
| W | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 | protein | 29 | 0% helix, 0% strand | F1S6Q1 |
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, A, O
- FMN · Flavin mononucleotide · ligand · chains A
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · chains A
- PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · chains C, J
- PLX · (9R,11S)-9-({[(1S)-1-hydroxyhexadecyl]oxy}methyl)-2,2-dimethyl-5,7,10-trioxa-2lambda~5~-aza-6lambda~5~-phosphaoctacosane-6,6,11-triol · ligand · chains B, C, N
- 8Q1 · S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy) butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate · ligand · chains E, G
- CDL · Cardiolipin · ligand · chains B, I, N
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains C, J
- MG · Magnesium ion · metal · chains M
- ZN · Zinc ion · metal · chains T
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 | 1192 | 0.90 | 0.91 | 151 | empty |
| 2 | 881 | 0.86 | 0.87 | 99 | 8Q1 |
| 3 | 874 | 0.85 | 0.87 | 89 | NDP |
| 4 | 492 | 0.83 | 0.90 | 61 | empty |
| 5 | 540 | 0.81 | 0.87 | 95 | empty |
Interfaces
63 interfaces between chains.
- A–O · 3260 Ų buried · 43 hydrogen bonds · protein-protein
- P–Q · 2700 Ų buried · 43 hydrogen bonds · protein-protein
- B–Q · 2270 Ų buried · 41 hydrogen bonds · protein-protein
- L–M · 2147 Ų buried · 31 hydrogen bonds · protein-protein
- B–N · 2136 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 disulfide, 1 modified (covalent ligand, disulfide, methylation).
Compared structures
- 7VWJ · Matrix arm of deactive state CI from rote -NADH dataset · the same entry in another collection · chain A against A, 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 F1RVN1
- Every structure of UniProt A0A287BDC0
- Every structure of UniProt I3LK43
- Every structure of UniProt A0A480VKQ8
- Every structure of UniProt F1RGE3
- Every structure of UniProt D0G781
- Every structure of UniProt A0A5G2RN85
- Every structure of UniProt A0A4X1VLA2
- Every structure of UniProt A0A480QJC4
- Every structure of UniProt A0A4X1TFI3
- Every structure of UniProt G8IFA6
- Every structure of UniProt F1SHD7
- Every structure of UniProt F1SQP4
- Every structure of UniProt A0A287BG40
- Every structure of UniProt A0A286ZNN4
- Every structure of UniProt A0A480JYS1
- Every structure of UniProt F1S031
- Every structure of UniProt F1S6Q1
- Elsewhere: RCSB PDB 7VWJ · PDBe 7VWJ · UniProt F1RVN1 · UniProt A0A287BDC0 · UniProt I3LK43 · UniProt A0A480VKQ8 · UniProt F1RGE3 · UniProt D0G781 · UniProt A0A5G2RN85 · UniProt A0A4X1VLA2 · UniProt A0A480QJC4 · UniProt A0A4X1TFI3 · UniProt G8IFA6 · UniProt F1SHD7 · UniProt F1SQP4 · UniProt A0A287BG40 · UniProt A0A286ZNN4 · UniProt A0A480JYS1 · UniProt F1S031 · UniProt F1S6Q1
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