Research workbench
Cryo-EM structure of cyanobacteria ndh-1LDELV complex
Analyse Cryo-EM structure of cyanobacteria ndh-1LDELV complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6L7P
- Type
- protein
- Length
- 3,896 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
- AJP, LHG, SQD, BCR, SF4, DGD, PQN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 18 distinct chains · 54% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD(P)H-quinone oxidoreductase subunit 1 (EC 7.1.1.-) | protein | 365 | 67% helix, 1% strand | Q8DL32 |
| B | NAD(P)H-quinone oxidoreductase subunit 2 (EC 7.1.1.-) | protein | 492 | 72% helix, 1% strand | Q8DMR6 |
| C | NAD(P)H-quinone oxidoreductase subunit 3 (EC 7.1.1.-) | protein | 121 | 57% helix, 0% strand | Q8DJ02 |
| D | NAD(P)H-quinone oxidoreductase chain 4 1 (EC 7.1.1.-) | protein | 504 | 66% helix, 2% strand | Q8DKY0 |
| E | NAD(P)H-quinone oxidoreductase subunit 4L (EC 7.1.1.-) | protein | 101 | 75% helix, 0% strand | Q8DL29 |
| F | NADH dehydrogenase subunit 5 | protein | 646 | 69% helix, 2% strand | Q8DKX9 |
| G | NADH-quinone oxidoreductase subunit J (EC 7.1.1.-) | protein | 191 | 64% helix, 0% strand | Q8DL30 |
| H | NAD(P)H-quinone oxidoreductase subunit H (EC 7.1.1.-) | protein | 393 | 41% helix, 9% strand | Q8DJD9 |
| I | NAD(P)H-quinone oxidoreductase subunit I (EC 7.1.1.-) | protein | 189 | 21% helix, 12% strand | Q8DL31 |
| J | NAD(P)H-quinone oxidoreductase subunit J (EC 7.1.1.-) | protein | 156 | 17% helix, 23% strand | Q8DJ01 |
| K | NAD(P)H-quinone oxidoreductase subunit K (EC 7.1.1.-) | protein | 200 | 30% helix, 15% strand | Q8DKZ4 |
| L | NAD(P)H-quinone oxidoreductase subunit L (EC 7.1.1.-) | protein | 73 | 68% helix, 0% strand | Q8DKZ3 |
| M | NAD(P)H-quinone oxidoreductase subunit M (EC 7.1.1.-) | protein | 110 | 33% helix, 22% strand | Q8DLN5 |
| N | NAD(P)H-quinone oxidoreductase subunit N (EC 7.1.1.-) | protein | 148 | 32% helix, 20% strand | Q8DJU2 |
| O | NAD(P)H-quinone oxidoreductase subunit O (EC 7.1.1.-) | protein | 67 | 10% helix, 31% strand | Q8DMU4 |
| P | NAD(P)H-quinone oxidoreductase subunit P | protein | 41 | 41% helix, 0% strand | — |
| Q | NAD(P)H-quinone oxidoreductase subunit Q | protein | 44 | 57% helix, 0% strand | — |
| S | TLR0636 protein | protein | 55 | 0% helix, 56% strand | Q8DL61 |
Ligands and binding sites
- AJP · Digitonin · ligand · 44 copies · chains A, B, D, C, F, I, P, Q, G, E
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 9 copies · chains A, H, I, C, G, B, D, F, P
- SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · 4 copies · chains D, F, Q, B, A, C, K, L, N
- BCR · Beta-carotene · ligand · 3 copies · chains A, I, L, D, F, P, Q
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains I, H, K
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 2 copies · chains A, C, L
- PQN · Phylloquinone · ligand · chains B
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 | 1079 | 0.88 | 0.89 | 103 | empty |
| 2 | 815 | 0.84 | 0.86 | 84 | empty |
| 3 | 1038 | 0.82 | 0.83 | 82 | AJP, SQD |
| 4 | 156 | 0.80 | 0.96 | 28 | empty |
| 5 | 385 | 0.80 | 0.89 | 56 | empty |
Interfaces
53 interfaces between chains.
- E–G · 3383 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 2946 Ų buried · 7 hydrogen bonds · protein-protein
- D–F · 2621 Ų buried · 9 hydrogen bonds · protein-protein
- B–G · 2527 Ų buried · 16 hydrogen bonds · protein-protein
- K–M · 2382 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 covalent (covalent ligand).
Compared structures
- 6L7P · cryo-EM structure of cyanobacteria NDH-1LdelV complex · 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 6L7P · PDBe 6L7P · 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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