Research workbench
Structure of the ndh-1MS complex from thermosynechococcus elongatus
Analyse Structure of the ndh-1MS complex from thermosynechococcus elongatus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TJV
- Type
- protein
- Length
- 4,274 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, Q8DKF4, Q8DL29, Q8DKF5, Q8DL30, Q8DJD9, Q8DL31, Q8DJ01, Q8DKZ4, Q8DKZ3, Q8DLN5, Q8DJU2, Q8DMU4, Q8DKF3, Q8DMA1, Q8DL61
- Ligands
- SQD, SF4, DGD, PGT, BCR, CLA, ZN
- Pockets
- 20 · best druggability 0.88
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 7.1.1.-) | protein | 361 | 58% helix, 0% strand | Q8DL32 |
| B | NAD(P)H-quinone oxidoreductase subunit 2 (EC 7.1.1.-) | protein | 475 | 70% helix, 1% strand | Q8DMR6 |
| C | NAD(P)H-quinone oxidoreductase subunit 3 (EC 7.1.1.-) | protein | 114 | 61% helix, 0% strand | Q8DJ02 |
| D | NADH dehydrogenase subunit 4 | protein | 478 | 68% helix, 3% strand | Q8DKF4 |
| E | NAD(P)H-quinone oxidoreductase subunit 4L (EC 7.1.1.-) | protein | 100 | 79% helix, 0% strand | Q8DL29 |
| F | NADH dehydrogenase subunit 5 | protein | 600 | 68% helix, 3% strand | Q8DKF5 |
| G | NADH dehydrogenase subunit 6 (EC 7.1.1.-) | protein | 168 | 75% 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 | 193 | 30% helix, 11% strand | Q8DL31 |
| J | NAD(P)H-quinone oxidoreductase subunit J (EC 7.1.1.-) | protein | 156 | 14% helix, 16% strand | Q8DJ01 |
| K | NAD(P)H-quinone oxidoreductase subunit K (EC 7.1.1.-) | protein | 206 | 31% helix, 11% strand | Q8DKZ4 |
| L | NAD(P)H-quinone oxidoreductase subunit L (EC 7.1.1.-) | protein | 76 | 70% helix, 0% strand | Q8DKZ3 |
| M | NAD(P)H-quinone oxidoreductase subunit M (EC 7.1.1.-) | protein | 110 | 33% helix, 15% strand | Q8DLN5 |
| N | NAD(P)H-quinone oxidoreductase subunit N (EC 7.1.1.-) | protein | 147 | 27% helix, 14% strand | Q8DJU2 |
| O | NAD(P)H-quinone oxidoreductase subunit O (EC 7.1.1.-) | protein | 68 | 9% helix, 22% strand | Q8DMU4 |
| P | TLR0906 protein | protein | 426 | 50% helix, 2% strand | Q8DKF3 |
| Q | TLL0220 protein | protein | 148 | 28% helix, 8% strand | Q8DMA1 |
| S | TLR0636 protein | protein | 55 | 0% helix, 45% strand | Q8DL61 |
Ligands and binding sites
- SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · 5 copies · chains D, F, P, A, C, 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
- PGT · (1S)-2-{[{[(2R)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate · ligand · 2 copies · chains A, C, G, B, D, F
- BCR · Beta-carotene · ligand · chains F, P
- CLA · Chlorophyll A · ligand · chains F
- ZN · Zinc ion · metal · chains 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 | 545 | 0.88 | 0.94 | 72 | empty |
| 2 | 1170 | 0.86 | 0.87 | 142 | empty |
| 3 | 440 | 0.85 | 0.92 | 53 | empty |
| 4 | 256 | 0.84 | 0.96 | 44 | empty |
| 5 | 154 | 0.80 | 0.97 | 25 | empty |
Interfaces
52 interfaces between chains.
- E–G · 3441 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 2992 Ų buried · 14 hydrogen bonds · protein-protein
- F–P · 2625 Ų buried · 19 hydrogen bonds · protein-protein
- K–M · 2336 Ų buried · 34 hydrogen bonds · protein-protein
- D–F · 2304 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6TJV · Structure of the NDH-1MS complex 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 Q8DMR6
- Every structure of UniProt Q8DJ02
- Every structure of UniProt Q8DKF4
- Every structure of UniProt Q8DL29
- Every structure of UniProt Q8DKF5
- 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 Q8DKF3
- Every structure of UniProt Q8DMA1
- Every structure of UniProt Q8DL61
- Elsewhere: RCSB PDB 6TJV · PDBe 6TJV · UniProt Q8DL32 · UniProt Q8DMR6 · UniProt Q8DJ02 · UniProt Q8DKF4 · UniProt Q8DL29 · UniProt Q8DKF5 · UniProt Q8DL30 · UniProt Q8DJD9 · UniProt Q8DL31 · UniProt Q8DJ01 · UniProt Q8DKZ4 · UniProt Q8DKZ3 · UniProt Q8DLN5 · UniProt Q8DJU2 · UniProt Q8DMU4 · UniProt Q8DKF3 · UniProt Q8DMA1 · UniProt Q8DL61
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