MolNFT v1 · #151667 · protein
Structure of the photosynthetic complex I from thermosynechococcus elongatus
6HUM · NAD(P)H-quinone oxidoreductase subunit 1: “Structure of the photosynthetic complex I from thermosynechococcus elongatus”. Electron microscopy, 3 ligands (SF4, BCR, LMG), 20 pockets (best druggability 0.87). MolNFT v1 #151667 on…
- PDB
- 6HUM
- Type
- protein
- Length
- 3,793 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 3…
- EC
- 1.6.5.-
- UniProt
- Q8DL32, Q8DJ02, Q8DKY0, Q8DL29, Q8DMR6, Q8DL30, Q8DJ01, Q8DJD9, Q8DL31, Q8DKZ4, Q8DKZ3, Q8DKX9, Q8DJU2, Q8DLN5, Q8DL61, Q8DMU4
- Ligands
- SF4, BCR, LMG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 18 distinct chains · 53% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD(P)H-quinone oxidoreductase subunit 1 (EC 1.6.5.-) | protein | 352 | 63% helix, 0% strand | Q8DL32 |
| C | NAD(P)H-quinone oxidoreductase subunit 3 (EC 1.6.5.-) | protein | 114 | 54% helix, 2% strand | Q8DJ02 |
| D | NAD(P)H-quinone oxidoreductase chain 4 1 (EC 1.6.5.-) | protein | 488 | 65% helix, 1% strand | Q8DKY0 |
| E | NAD(P)H-quinone oxidoreductase subunit 4L (EC 1.6.5.-) | protein | 100 | 76% helix, 0% strand | Q8DL29 |
| B | NAD(P)H-quinone oxidoreductase subunit 2 (EC 1.6.5.-) | protein | 475 | 73% helix, 1% strand | Q8DMR6 |
| G | NADH dehydrogenase subunit 6 | protein | 168 | 71% helix, 0% strand | Q8DL30 |
| J | NAD(P)H-quinone oxidoreductase subunit J (EC 1.6.5.-) | protein | 156 | 21% helix, 12% strand | Q8DJ01 |
| P | Proton-translocating NADH-quinone dehydrogenase subunit P ndhp | protein | 42 | 50% helix, 0% strand | — |
| H | NAD(P)H-quinone oxidoreductase subunit H (EC 1.6.5.-) | protein | 393 | 41% helix, 7% strand | Q8DJD9 |
| I | NAD(P)H-quinone oxidoreductase subunit I (EC 1.6.5.-) | protein | 193 | 27% helix, 9% strand | Q8DL31 |
| K | NAD(P)H-quinone oxidoreductase subunit K (EC 1.6.5.-) | protein | 206 | 30% helix, 11% strand | Q8DKZ4 |
| L | NAD(P)H-quinone oxidoreductase subunit L (EC 1.6.5.-) | protein | 76 | 61% helix, 0% strand | Q8DKZ3 |
| F | NADH dehydrogenase subunit 5 | protein | 611 | 67% helix, 2% strand | Q8DKX9 |
| N | NAD(P)H-quinone oxidoreductase subunit N (EC 1.6.5.-) | protein | 147 | 20% helix, 10% strand | Q8DJU2 |
| M | NAD(P)H-quinone oxidoreductase subunit M (EC 1.6.5.-) | protein | 110 | 32% helix, 12% strand | Q8DLN5 |
| S | TLR0636 protein | protein | 55 | 5% helix, 47% strand | Q8DL61 |
| O | NAD(P)H-quinone oxidoreductase subunit O (EC 1.6.5.-) | protein | 68 | 4% helix, 24% strand | Q8DMU4 |
| Q | Proton-translocating NADH-quinone dehydrogenase subunit Q ndhq | protein | 39 | 59% helix, 0% strand | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains I, H, K
- BCR · Beta-carotene · ligand · chains D, P, F
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · chains D, F
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 | 1021 | 0.87 | 0.88 | 137 | empty |
| 2 | 444 | 0.86 | 0.93 | 46 | empty |
| 3 | 217 | 0.82 | 0.95 | 45 | empty |
| 4 | 1163 | 0.81 | 0.82 | 83 | LMG |
| 5 | 301 | 0.80 | 0.90 | 27 | BCR |
Interfaces
51 interfaces between chains.
- E–G · 3565 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 2908 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 2509 Ų buried · 17 hydrogen bonds · protein-protein
- K–M · 2459 Ų buried · 31 hydrogen bonds · protein-protein
- C–G · 2231 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6HUM · Structure of the photosynthetic complex I from Thermosynechococcus elongatus · 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 Q8DJ02
- Every structure of UniProt Q8DKY0
- Every structure of UniProt Q8DL29
- Every structure of UniProt Q8DMR6
- Every structure of UniProt Q8DL30
- Every structure of UniProt Q8DJ01
- Every structure of UniProt Q8DJD9
- Every structure of UniProt Q8DL31
- Every structure of UniProt Q8DKZ4
- Every structure of UniProt Q8DKZ3
- Every structure of UniProt Q8DKX9
- Every structure of UniProt Q8DJU2
- Every structure of UniProt Q8DLN5
- Every structure of UniProt Q8DL61
- Every structure of UniProt Q8DMU4
- Elsewhere: RCSB PDB 6HUM · PDBe 6HUM · UniProt Q8DL32 · UniProt Q8DJ02 · UniProt Q8DKY0 · UniProt Q8DL29 · UniProt Q8DMR6 · UniProt Q8DL30 · UniProt Q8DJ01 · UniProt Q8DJD9 · UniProt Q8DL31 · UniProt Q8DKZ4 · UniProt Q8DKZ3 · UniProt Q8DKX9 · UniProt Q8DJU2 · UniProt Q8DLN5 · UniProt Q8DL61 · UniProt Q8DMU4
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