Research workbench
Deactive state complex I from rote -NADH dataset
Analyse Deactive state complex I from rote -NADH dataset in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7V3M
- Type
- protein
- Length
- 8,140 residues
- Chains
- 45
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.9
- Source
- Sus scrofa
- 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, K7GR43, F1S031, A0A4X1VQ42, I3LGM4, F1S6Q1, A0A4X1V766, A0A287AS93, F1SGC6, Q2EN80, F1RWL7, A0A4X1VYV0, A1XQS6, A0A480JRW3, F1SV23, O79875, O79880, P56632, Q71K68, O79882, F1SD73, A0A4X1T6M0, A0A4X1T0A8, Q7IIB7, O79874, F1SLR1, F1SCH1, F1SIS9
- Ligands
- PEE, CDL, SF4, PLX, 8Q1, FES, FMN, NAI, NDP, UQ, ADP, MG, ZN
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · resolution 2.9 · 44 distinct chains · 52% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (EC 7.1.1.2) | protein | 431 | 48% helix, 13% strand | F1RVN1 |
| B | NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial | protein | 176 | 38% helix, 17% strand | A0A287BDC0 |
| C | NADH dehydrogenase [ubiquinone] iron-sulfur protein 7,mitochondrial | protein | 156 | 52% 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 | 38% helix, 30% strand | F1RGE3 |
| G, X | Acyl carrier protein, mitochondrial | protein | 88 | 50% helix, 0% strand | D0G781 |
| H | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 | protein | 112 | 55% helix, 0% strand | A0A5G2RN85 |
| I | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 | protein | 97 | 18% helix, 6% strand | A0A4X1VLA2 |
| J | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial | protein | 297 | 39% helix, 15% strand | A0A480QJC4 |
| K | NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial | protein | 42 | 38% helix, 2% strand | A0A4X1TFI3 |
| L | NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial | protein | 125 | 14% 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 | 38% 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 | 419 | 49% helix, 13% strand | A0A480JYS1 |
| S | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 | protein | 70 | 63% helix, 0% strand | K7GR43 |
| T | NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial | protein | 96 | 16% helix, 20% strand | F1S031 |
| U | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 | protein | 83 | 52% helix, 2% strand | A0A4X1VQ42 |
| V | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 | protein | 140 | 79% helix, 0% strand | I3LGM4 |
| W | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 | protein | 142 | 61% helix, 1% strand | F1S6Q1 |
| Y | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial | protein | 70 | 46% helix, 0% strand | A0A4X1V766 |
| Z | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 | protein | 84 | 45% helix, 0% strand | A0A287AS93 |
| a | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial | protein | 140 | 59% helix, 3% strand | F1SGC6 |
| b | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 | protein | 103 | 45% helix, 7% strand | Q2EN80 |
| c | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial | protein | 156 | 26% helix, 4% strand | F1RWL7 |
| d | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 | protein | 175 | 67% helix, 3% strand | A0A4X1VYV0 |
| e | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial | protein | 107 | 49% helix, 1% strand | — |
| f | NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial | protein | 42 | 79% helix, 0% strand | A1XQS6 |
| g | NADH dehydrogenase [ubiquinone] 1 subunit C2 | protein | 121 | 58% helix, 2% strand | A0A480JRW3 |
| h | NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 | protein | 105 | 62% helix, 0% strand | F1SV23 |
| i | NADH-ubiquinone oxidoreductase chain 2 (EC 7.1.1.2) | protein | 347 | 75% helix, 2% strand | O79875 |
| j | NADH-ubiquinone oxidoreductase chain 3 (EC 7.1.1.2) | protein | 99 | 74% helix, 0% strand | O79880 |
| k | NADH-ubiquinone oxidoreductase chain 4L (EC 7.1.1.2) | protein | 98 | 81% helix, 0% strand | P56632 |
| l | NADH-ubiquinone oxidoreductase chain 5 (EC 7.1.1.2) | protein | 603 | 73% helix, 4% strand | Q71K68 |
| m | NADH-ubiquinone oxidoreductase chain 6 (EC 7.1.1.2) | protein | 129 | 73% helix, 0% strand | O79882 |
| n | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 | protein | 56 | 45% helix, 0% strand | F1SD73 |
| o | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 | protein | 128 | 63% helix, 0% strand | A0A4X1T6M0 |
| p | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 | protein | 178 | 53% helix, 0% strand | A0A4X1T0A8 |
| r | NADH-ubiquinone oxidoreductase chain 4 (EC 7.1.1.2) | protein | 459 | 73% helix, 1% strand | Q7IIB7 |
| s | NADH-ubiquinone oxidoreductase chain 1 (EC 7.1.1.2) | protein | 303 | 69% helix, 1% strand | O79874 |
| u | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 | protein | 171 | 44% helix, 2% strand | F1SLR1 |
| v | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 | protein | 124 | 60% helix, 1% strand | F1SCH1 |
| w | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial | protein | 320 | 49% helix, 8% strand | F1SIS9 |
Ligands and binding sites
- PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · 8 copies · chains B, Q, U, W, s, C, J, j, i, l, r, S, m, c, b, V
- CDL · Cardiolipin · ligand · 7 copies · chains I, N, S, s, a, b, d, e, l, r, i, w, c, g, n, u
- SF4 · Iron/sulfur cluster · ligand · 6 copies · chains A, B, C, Q, M
- 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 · 6 copies · chains B, C, N, s, a, e, n, r, g, h, i, j, m, V, l
- 8Q1 · S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy) butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate · ligand · 2 copies · chains E, G, X, l, p
- 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
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains C, J
- UQ · Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer · ligand · chains C, s
- ADP · Adenosine-5'-diphosphate · ligand · chains w
- MG · Magnesium ion · metal · chains L, 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 | 1030 | 0.90 | 0.92 | 109 | PEE |
| 2 | 1036 | 0.89 | 0.91 | 119 | empty |
| 3 | 900 | 0.86 | 0.87 | 110 | 8Q1 |
| 4 | 533 | 0.85 | 0.91 | 86 | empty |
| 5 | 440 | 0.85 | 0.92 | 68 | empty |
Interfaces
201 interfaces between chains.
- A–O · 3182 Ų buried · 42 hydrogen bonds · protein-protein
- j–s · 2697 Ų buried · 6 hydrogen bonds · protein-protein
- P–Q · 2688 Ų buried · 37 hydrogen bonds · protein-protein
- k–m · 2475 Ų buried · 6 hydrogen bonds · protein-protein
- l–r · 2346 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 covalent, 1 modified (disulfide, covalent ligand, methylation).
Compared structures
- 7V3M · Deactive state complex I from rotenone-NADH dataset · 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 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 K7GR43
- Every structure of UniProt F1S031
- Every structure of UniProt A0A4X1VQ42
- Every structure of UniProt I3LGM4
- Every structure of UniProt F1S6Q1
- Every structure of UniProt A0A4X1V766
- Every structure of UniProt A0A287AS93
- Every structure of UniProt F1SGC6
- Every structure of UniProt Q2EN80
- Every structure of UniProt F1RWL7
- Every structure of UniProt A0A4X1VYV0
- Every structure of UniProt A1XQS6
- Every structure of UniProt A0A480JRW3
- Every structure of UniProt F1SV23
- Every structure of UniProt O79875
- Every structure of UniProt O79880
- Every structure of UniProt P56632
- Every structure of UniProt Q71K68
- Every structure of UniProt O79882
- Every structure of UniProt F1SD73
- Every structure of UniProt A0A4X1T6M0
- Every structure of UniProt A0A4X1T0A8
- Every structure of UniProt Q7IIB7
- Every structure of UniProt O79874
- Every structure of UniProt F1SLR1
- Every structure of UniProt F1SCH1
- Every structure of UniProt F1SIS9
- Elsewhere: RCSB PDB 7V3M · PDBe 7V3M · 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 K7GR43 · UniProt F1S031 · UniProt A0A4X1VQ42 · UniProt I3LGM4 · UniProt F1S6Q1 · UniProt A0A4X1V766 · UniProt A0A287AS93 · UniProt F1SGC6 · UniProt Q2EN80 · UniProt F1RWL7 · UniProt A0A4X1VYV0 · UniProt A1XQS6 · UniProt A0A480JRW3 · UniProt F1SV23 · UniProt O79875 · UniProt O79880 · UniProt P56632 · UniProt Q71K68 · UniProt O79882 · UniProt F1SD73 · UniProt A0A4X1T6M0 · UniProt A0A4X1T0A8 · UniProt Q7IIB7 · UniProt O79874 · UniProt F1SLR1 · UniProt F1SCH1 · UniProt F1SIS9
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