Research workbench
Membrane arm of deactive state ci from dq-NADH dataset
Analyse Membrane arm of deactive state ci from dq-NADH dataset in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VBP
- Type
- protein
- Length
- 4,652 residues
- Chains
- 29
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial; NADH dehydrogenase…
- EC
- 7.1.1.2
- UniProt
- A0A480JYS1, K7GR43, A0A4X1VQ42, I3LGM4, F1S6Q1, D0G781, 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, PLX, 8Q1, UQ, ADP
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · 29 distinct chains · 63% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Q | NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial | protein | 40 | 18% helix, 3% strand | A0A480JYS1 |
| S | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 | protein | 70 | 64% helix, 0% strand | K7GR43 |
| 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 | 113 | 76% helix, 1% strand | F1S6Q1 |
| X | Acyl carrier protein, mitochondrial | protein | 88 | 53% helix, 0% strand | D0G781 |
| Y | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial | protein | 70 | 50% helix, 0% strand | A0A4X1V766 |
| Z | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 | protein | 84 | 52% 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, 6% strand | Q2EN80 |
| c | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial | protein | 156 | 28% 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 | 50% helix, 1% strand | — |
| f | NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial | protein | 42 | 76% helix, 0% strand | A1XQS6 |
| g | NADH dehydrogenase [ubiquinone] 1 subunit C2 | protein | 121 | 57% helix, 2% strand | A0A480JRW3 |
| h | NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 | protein | 105 | 60% helix, 0% strand | F1SV23 |
| i | NADH-ubiquinone oxidoreductase chain 2 (EC 7.1.1.2) | protein | 347 | 74% 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 | 80% helix, 0% strand | P56632 |
| l | NADH-ubiquinone oxidoreductase chain 5 (EC 7.1.1.2) | protein | 603 | 75% 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 | 60% helix, 0% strand | A0A4X1T6M0 |
| p | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 | protein | 178 | 55% helix, 0% strand | A0A4X1T0A8 |
| r | NADH-ubiquinone oxidoreductase chain 4 (EC 7.1.1.2) | protein | 459 | 74% helix, 2% 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 | 49% 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 | 48% helix, 8% strand | F1SIS9 |
Ligands and binding sites
- PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · 7 copies · chains Q, i, l, r, U, j, s, b, c, S, W, m, V
- CDL · Cardiolipin · ligand · 6 copies · chains V, l, o, r, a, b, d, e, g, i, n, u, c, p, w
- 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 · 5 copies · chains 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 · chains X, l, p
- UQ · Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer · ligand · chains s
- ADP · Adenosine-5'-diphosphate · ligand · chains w
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 | 1062 | 0.90 | 0.91 | 119 | PEE |
| 2 | 988 | 0.88 | 0.89 | 101 | empty |
| 3 | 1075 | 0.88 | 0.89 | 87 | empty |
| 4 | 767 | 0.87 | 0.91 | 119 | empty |
| 5 | 542 | 0.85 | 0.91 | 63 | empty |
Interfaces
122 interfaces between chains.
- j–s · 2641 Ų buried · 8 hydrogen bonds · protein-protein
- k–m · 2423 Ų buried · 7 hydrogen bonds · protein-protein
- l–r · 2383 Ų buried · 15 hydrogen bonds · protein-protein
- c–o · 2131 Ų buried · 31 hydrogen bonds · protein-protein
- W–u · 1905 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 7VBP · Membrane arm of deactive state CI from DQ-NADH dataset · the same entry in another collection · chain c against c, 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 A0A480JYS1
- Every structure of UniProt K7GR43
- Every structure of UniProt A0A4X1VQ42
- Every structure of UniProt I3LGM4
- Every structure of UniProt F1S6Q1
- Every structure of UniProt D0G781
- 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 7VBP · PDBe 7VBP · UniProt A0A480JYS1 · UniProt K7GR43 · UniProt A0A4X1VQ42 · UniProt I3LGM4 · UniProt F1S6Q1 · UniProt D0G781 · 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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