MolNFT v1 · #154629 · protein
Supercomplex for electron transfer
6KHJ · NAD(P)H-quinone oxidoreductase subunit 1: “Supercomplex for electron transfer”. Electron microscopy, 7 ligands (LHG, SQD, SF4), 20 pockets (best druggability 0.87). MolNFT v1 #154629 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6KHJ
- Type
- protein
- Length
- 3,877 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD(P)H-quinone oxidoreductase subunit 1; NAD(P)H-quinone oxidoreductase subunit 2…
- EC
- 7.1.1.-
- UniProt
- Q8DL32, Q8DMR6, Q8DJ02, Q8DKY0, Q8DL29, Q8DKX9, Q8DL30, Q8DJD9, Q8DL31, Q8DJ01, Q8DKZ4, Q8DKZ3, Q8DLN5, Q8DJU2, Q8DMU4, Q8DL61
- Ligands
- LHG, SQD, SF4, DGD, BCR, LMG, PL9
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 18 distinct chains · 55% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD(P)H-quinone oxidoreductase subunit 1 (EC 7.1.1.-) | protein | 369 | 64% helix, 0% strand | Q8DL32 |
| B | NAD(P)H-quinone oxidoreductase subunit 2 (EC 7.1.1.-) | protein | 488 | 74% helix, 1% strand | Q8DMR6 |
| C | NAD(P)H-quinone oxidoreductase subunit 3 (EC 7.1.1.-) | protein | 120 | 61% helix, 3% strand | Q8DJ02 |
| D | NAD(P)H-quinone oxidoreductase chain 4 1 (EC 7.1.1.-) | protein | 504 | 68% helix, 4% strand | Q8DKY0 |
| E | NAD(P)H-quinone oxidoreductase subunit 4L (EC 7.1.1.-) | protein | 101 | 76% helix, 2% strand | Q8DL29 |
| F | NADH dehydrogenase subunit 5 | protein | 639 | 70% helix, 3% strand | Q8DKX9 |
| G | NADH-quinone oxidoreductase subunit J (EC 7.1.1.-) | protein | 170 | 73% helix, 0% strand | Q8DL30 |
| H | NAD(P)H-quinone oxidoreductase subunit H (EC 7.1.1.-) | protein | 393 | 44% helix, 8% strand | Q8DJD9 |
| I | NAD(P)H-quinone oxidoreductase subunit I (EC 7.1.1.-) | protein | 189 | 22% helix, 13% strand | Q8DL31 |
| J | NAD(P)H-quinone oxidoreductase subunit J (EC 7.1.1.-) | protein | 158 | 18% helix, 20% strand | Q8DJ01 |
| K | NAD(P)H-quinone oxidoreductase subunit K (EC 7.1.1.-) | protein | 204 | 29% helix, 11% strand | Q8DKZ4 |
| L | NAD(P)H-quinone oxidoreductase subunit L (EC 7.1.1.-) | protein | 73 | 70% helix, 0% strand | Q8DKZ3 |
| M | NAD(P)H-quinone oxidoreductase subunit M (EC 7.1.1.-) | protein | 111 | 34% helix, 13% strand | Q8DLN5 |
| N | NAD(P)H-quinone oxidoreductase subunit N (EC 7.1.1.-) | protein | 145 | 31% helix, 19% strand | Q8DJU2 |
| O | NAD(P)H-quinone oxidoreductase subunit O (EC 7.1.1.-) | protein | 68 | 10% helix, 32% strand | Q8DMU4 |
| P | Proton-translocating NADH-quinone dehydrogenase subunit P | protein | 41 | 46% helix, 0% strand | — |
| Q | Proton-translocating NADH-quinone dehydrogenase subunit Q | protein | 44 | 55% helix, 0% strand | — |
| S | TLR0636 protein | protein | 60 | 5% helix, 45% strand | Q8DL61 |
Ligands and binding sites
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 6 copies · chains A, B, C, D, F, P, Q, I
- SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · 3 copies · chains B, D, F, A, C, G, K, L, N
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains I, H, K
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 2 copies · chains A, C, L
- BCR · Beta-carotene · ligand · 2 copies · chains D, F, P, Q
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 2 copies · chains D, F
- PL9 · 2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2, 6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone · ligand · chains A, H, K
- LMT · Dodecyl-beta-D-maltoside · additive · chains B, D
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 | 1162 | 0.87 | 0.88 | 98 | PL9 |
| 2 | 894 | 0.82 | 0.84 | 77 | LMG |
| 3 | 327 | 0.80 | 0.90 | 50 | empty |
| 4 | 255 | 0.80 | 0.91 | 27 | BCR |
| 5 | 115 | 0.79 | 0.97 | 29 | empty |
Interfaces
54 interfaces between chains.
- E–G · 3419 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 3086 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 2713 Ų buried · 24 hydrogen bonds · protein-protein
- K–M · 2530 Ų buried · 44 hydrogen bonds · protein-protein
- C–G · 2151 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6KHJ · Supercomplex for electron transfer · the same entry in another collection · chain K against K, 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 Q8DL32
- Every structure of UniProt Q8DMR6
- Every structure of UniProt Q8DJ02
- Every structure of UniProt Q8DKY0
- Every structure of UniProt Q8DL29
- Every structure of UniProt Q8DKX9
- Every structure of UniProt Q8DL30
- Every structure of UniProt Q8DJD9
- Every structure of UniProt Q8DL31
- Every structure of UniProt Q8DJ01
- Every structure of UniProt Q8DKZ4
- Every structure of UniProt Q8DKZ3
- Every structure of UniProt Q8DLN5
- Every structure of UniProt Q8DJU2
- Every structure of UniProt Q8DMU4
- Every structure of UniProt Q8DL61
- Elsewhere: RCSB PDB 6KHJ · PDBe 6KHJ · UniProt Q8DL32 · UniProt Q8DMR6 · UniProt Q8DJ02 · UniProt Q8DKY0 · UniProt Q8DL29 · UniProt Q8DKX9 · UniProt Q8DL30 · UniProt Q8DJD9 · UniProt Q8DL31 · UniProt Q8DJ01 · UniProt Q8DKZ4 · UniProt Q8DKZ3 · UniProt Q8DLN5 · UniProt Q8DJU2 · UniProt Q8DMU4 · UniProt Q8DL61
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