MolNFT v1 · #177794 · protein
Chloroplast ndh complex
7EU3 · NAD(P)H-quinone oxidoreductase subunit 1, chloroplastic: “Chloroplast ndh complex”. Electron microscopy, 4 ligands (SQD, LHG, BCR), 20 pockets (best druggability 0.88). MolNFT v1 #177794 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7EU3
- Type
- protein
- Length
- 5,399 residues
- Chains
- 25
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD(P)H-quinone oxidoreductase subunit 1, chloroplastic; NAD(P)H-quinone oxidoreductase…
- EC
- 7.1.1.-
- UniProt
- P92432, S4Z268, S4Z1L1, S4Z8N2, A0A218LNA9, A0A4Y5SEJ9, S4Z272, A0A218LNN1, S4Z232
- Ligands
- SQD, LHG, BCR, SF4
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 25 distinct chains · 42% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD(P)H-quinone oxidoreductase subunit 1, chloroplastic (EC 7.1.1.-) | protein | 346 | 58% helix, 0% strand | P92432 |
| B | NAD(P)H-quinone oxidoreductase subunit 2, chloroplastic (EC 7.1.1.-) | protein | 478 | 67% helix, 0% strand | S4Z268 |
| C | NAD(P)H-quinone oxidoreductase subunit 3, chloroplastic (EC 7.1.1.-) | protein | 116 | 61% helix, 0% strand | S4Z1L1 |
| D | NAD(P)H-quinone oxidoreductase chain 4, chloroplastic (EC 7.1.1.-) | protein | 499 | 63% helix, 2% strand | S4Z8N2 |
| E | NAD(P)H-quinone oxidoreductase subunit 4L, chloroplastic (EC 7.1.1.-) | protein | 100 | 75% helix, 2% strand | A0A218LNA9 |
| F | NAD(P)H-quinone oxidoreductase subunit F | protein | 671 | 62% helix, 3% strand | — |
| G | NAD(P)H-quinone oxidoreductase subunit 6, chloroplastic (EC 7.1.1.-) | protein | 176 | 70% helix, 0% strand | A0A4Y5SEJ9 |
| H | NAD(P)H-quinone oxidoreductase subunit H, chloroplastic (EC 7.1.1.-) | protein | 383 | 41% helix, 7% strand | S4Z272 |
| I | NAD(P)H-quinone oxidoreductase subunit I, chloroplastic (EC 7.1.1.-) | protein | 165 | 22% helix, 2% strand | A0A218LNN1 |
| J | NAD(P)H-quinone oxidoreductase subunit J | protein | 159 | 16% helix, 19% strand | — |
| K | NAD(P)H-quinone oxidoreductase subunit K, chloroplastic (EC 7.1.1.-) | protein | 194 | 26% helix, 8% strand | S4Z232 |
| L | NAD(P)H-quinone oxidoreductase subunit L | protein | 69 | 59% helix, 0% strand | — |
| M | NAD(P)H-quinone oxidoreductase subunit M | protein | 112 | 31% helix, 7% strand | — |
| N | NAD(P)H-quinone oxidoreductase subunit N | protein | 145 | 20% helix, 13% strand | — |
| T | Unidentified stromal protein | protein | 61 | 0% helix, 0% strand | — |
| 1 | Photosynthetic ndh subunit of subcomplex L1 | protein | 150 | 15% helix, 25% strand | — |
| 2 | Photosynthetic ndh subunit of subcomplex L2 | protein | 129 | 52% helix, 0% strand | — |
| 3 | Photosynthetic ndh subunit of subcomplex L3 | protein | 134 | 57% helix, 0% strand | — |
| 4 | Photosynthetic ndh subunit of subcomplex L4 | protein | 130 | 7% helix, 26% strand | — |
| 5 | Photosynthetic ndh subunit of subcomplex L5 | protein | 172 | 10% helix, 28% strand | — |
| 6 | Photosynthetic ndh subunit of subcomplex B1 | protein | 343 | 28% helix, 9% strand | — |
| 7 | Photosynthetic ndh subunit of subcomplex B2 | protein | 317 | 0% helix, 27% strand | — |
| 8 | Photosynthetic ndh subunit of subcomplex B3 | protein | 119 | 9% helix, 17% strand | — |
| 9 | Photosynthetic ndh subunit of subcomplex B4 | protein | 82 | 34% helix, 5% strand | — |
| 0 | Photosynthetic ndh subunit of subcomplex B5 | protein | 149 | 35% helix, 0% strand | — |
Ligands and binding sites
- SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · 2 copies · chains D, F, 0
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · chains D, F, 9, 0
- BCR · Beta-carotene · ligand · chains D, F, 9
- SF4 · Iron/sulfur cluster · ligand · chains F, 8
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 | 1117 | 0.88 | 0.89 | 124 | empty |
| 2 | 1128 | 0.88 | 0.89 | 109 | empty |
| 3 | 462 | 0.86 | 0.92 | 80 | empty |
| 4 | 679 | 0.85 | 0.89 | 73 | empty |
| 5 | 525 | 0.84 | 0.90 | 72 | empty |
Interfaces
76 interfaces between chains.
- E–G · 3088 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 2736 Ų buried · 6 hydrogen bonds · protein-protein
- D–F · 2499 Ų buried · 7 hydrogen bonds · protein-protein
- K–M · 2224 Ų buried · 18 hydrogen bonds · protein-protein
- C–G · 1928 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7EU3 · Chloroplast NDH complex · the same entry in another collection · chain A against A, 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 P92432
- Every structure of UniProt S4Z268
- Every structure of UniProt S4Z1L1
- Every structure of UniProt S4Z8N2
- Every structure of UniProt A0A218LNA9
- Every structure of UniProt A0A4Y5SEJ9
- Every structure of UniProt S4Z272
- Every structure of UniProt A0A218LNN1
- Every structure of UniProt S4Z232
- Elsewhere: RCSB PDB 7EU3 · PDBe 7EU3 · UniProt P92432 · UniProt S4Z268 · UniProt S4Z1L1 · UniProt S4Z8N2 · UniProt A0A218LNA9 · UniProt A0A4Y5SEJ9 · UniProt S4Z272 · UniProt A0A218LNN1 · UniProt S4Z232
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