MolNFT v1 · #139887 · protein
Cryo-EM structure of human respiratory complex I transmembrane arm
5XTC · NADH dehydrogenase [ubiquinone] iron-sulfur protein 2…: “Cryo-EM structure of human respiratory complex I transmembrane arm”. Electron microscopy, 4 ligands (PLX, CDL, PEE), 20 pockets (best druggability 0.86). MolNFT v1 #139887 on…
- PDB
- 5XTC
- Type
- protein
- Length
- 4,701 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
- 1.6.5.3, 1.6.99.3
- UniProt
- O75306, O15239, O95167, Q86Y39, Q9P0J0, O14561, O95178, O43676, O43674, O95139, O95169, O96000, Q9NX14, O43677, O95298, O43920, Q4GRX1, B9EE38, V9JN72, X5BVZ3, Q8HAX7, O75438, O95168, Q9Y6M9, B2XJG5, H9PGF0, P51970, P17568, O95299
- Ligands
- PLX, CDL, PEE, 8Q1
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 29 distinct chains · 62% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Q | NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial (EC 1.6.5.3, 1.6.99.3) | protein | 46 | 37% helix, 2% strand | O75306 |
| S | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 | protein | 70 | 66% helix, 0% strand | O15239 |
| U | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 | protein | 83 | 53% helix, 2% strand | O95167 |
| V | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 | protein | 140 | 78% helix, 0% strand | Q86Y39 |
| W | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 | protein | 116 | 65% helix, 0% strand | Q9P0J0 |
| X | Acyl carrier protein, mitochondrial | protein | 85 | 55% helix, 0% strand | O14561 |
| Y | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial | protein | 59 | 41% helix, 0% strand | O95178 |
| Z | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 | protein | 80 | 56% helix, 0% strand | O43676 |
| a | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial | protein | 138 | 57% helix, 1% strand | O43674 |
| b | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 | protein | 124 | 55% helix, 2% strand | O95139 |
| c | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial | protein | 153 | 31% helix, 2% strand | O95169 |
| d | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 | protein | 171 | 69% helix, 1% strand | O96000 |
| e | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial | protein | 97 | 52% helix, 0% strand | Q9NX14 |
| f | NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial | protein | 47 | 72% helix, 0% strand | O43677 |
| g | NADH dehydrogenase [ubiquinone] 1 subunit C2 | protein | 119 | 56% helix, 1% strand | O95298 |
| h | NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 | protein | 104 | 48% helix, 0% strand | O43920 |
| i | NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) | protein | 347 | 73% helix, 2% strand | Q4GRX1 |
| j | NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) | protein | 115 | 58% helix, 2% strand | B9EE38 |
| k | NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) | protein | 97 | 76% helix, 0% strand | V9JN72 |
| l | NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) | protein | 603 | 72% helix, 2% strand | X5BVZ3 |
| m | NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) | protein | 174 | 68% helix, 0% strand | Q8HAX7 |
| n | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 | protein | 56 | 52% helix, 0% strand | O75438 |
| o | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 | protein | 128 | 62% helix, 2% strand | O95168 |
| p | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 | protein | 172 | 55% helix, 0% strand | Q9Y6M9 |
| r | NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) | protein | 459 | 74% helix, 0% strand | B2XJG5 |
| s | NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) | protein | 318 | 68% helix, 1% strand | H9PGF0 |
| u | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 | protein | 169 | 43% helix, 1% strand | P51970 |
| v | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 | protein | 111 | 63% helix, 0% strand | P17568 |
| w | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial | protein | 320 | 49% helix, 5% strand | O95299 |
Ligands and binding sites
- 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 · 9 copies · chains U, j, s, V, l, o, a, b, d, e, r, g, h, i, f, W
- CDL · Cardiolipin · ligand · 5 copies · chains V, i, l, g, r, w, a, c, o, n, u
- PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · 4 copies · chains V, i, r, S, W, j, m, s, Q, l, c
- 8Q1 · S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy) butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate · ligand · chains X, p
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 | 1193 | 0.86 | 0.87 | 98 | empty |
| 2 | 1028 | 0.86 | 0.87 | 108 | empty |
| 3 | 1142 | 0.86 | 0.86 | 94 | empty |
| 4 | 842 | 0.86 | 0.88 | 106 | empty |
| 5 | 294 | 0.85 | 0.96 | 50 | empty |
Interfaces
124 interfaces between chains.
- k–m · 3003 Ų buried · 15 hydrogen bonds · protein-protein
- j–s · 2766 Ų buried · 11 hydrogen bonds · protein-protein
- l–r · 2188 Ų buried · 6 hydrogen bonds · protein-protein
- i–w · 1922 Ų buried · 21 hydrogen bonds · protein-protein
- c–o · 1897 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 5XTC · Cryo-EM structure of human respiratory complex I transmembrane arm · the same entry in another collection · chain Z against Z, 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 O75306
- Every structure of UniProt O15239
- Every structure of UniProt O95167
- Every structure of UniProt Q86Y39
- Every structure of UniProt Q9P0J0
- Every structure of UniProt O14561
- Every structure of UniProt O95178
- Every structure of UniProt O43676
- Every structure of UniProt O43674
- Every structure of UniProt O95139
- Every structure of UniProt O95169
- Every structure of UniProt O96000
- Every structure of UniProt Q9NX14
- Every structure of UniProt O43677
- Every structure of UniProt O95298
- Every structure of UniProt O43920
- Every structure of UniProt Q4GRX1
- Every structure of UniProt B9EE38
- Every structure of UniProt V9JN72
- Every structure of UniProt X5BVZ3
- Every structure of UniProt Q8HAX7
- Every structure of UniProt O75438
- Every structure of UniProt O95168
- Every structure of UniProt Q9Y6M9
- Every structure of UniProt B2XJG5
- Every structure of UniProt H9PGF0
- Every structure of UniProt P51970
- Every structure of UniProt P17568
- Every structure of UniProt O95299
- Elsewhere: RCSB PDB 5XTC · PDBe 5XTC · UniProt O75306 · UniProt O15239 · UniProt O95167 · UniProt Q86Y39 · UniProt Q9P0J0 · UniProt O14561 · UniProt O95178 · UniProt O43676 · UniProt O43674 · UniProt O95139 · UniProt O95169 · UniProt O96000 · UniProt Q9NX14 · UniProt O43677 · UniProt O95298 · UniProt O43920 · UniProt Q4GRX1 · UniProt B9EE38 · UniProt V9JN72 · UniProt X5BVZ3 · UniProt Q8HAX7 · UniProt O75438 · UniProt O95168 · UniProt Q9Y6M9 · UniProt B2XJG5 · UniProt H9PGF0 · UniProt P51970 · UniProt P17568 · UniProt O95299
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