Crystal structure of the cytochrome B6F complex with 2-nonyl-4- hydroxyquinoline N-oxide (nqno) from M.LAMINOSUS

Structure

x-ray diffraction · 8 distinct chains · 45% helix, 12% strand (DSSP).

Ligands and binding sites

• HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, H, C
• UMQ · Undecyl-maltoside · ligand · 4 copies · chains A, B, C, D
• OPC · (7R,17E)-4-hydroxy-N,N,N,7-tetramethyl-7-[(8E)-octadec-8-enoyloxy]-10-oxo-3,5,9-trioxa-4-phosphaheptacos-17-en-1-aminium 4-oxide · ligand · 2 copies · chains A, B, C, E, F, G, H
• QNO · 2-nonyl-4-hydroxyquinoline N-oxide · ligand · chains A, B
• CLA · Chlorophyll A · ligand · chains A, B
• FES · Fe2/s2 (inorganic) cluster · ligand · chains D
• SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · chains B, C, D
• BCR · Beta-carotene · ligand · chains A, B, F, G, H
• CD · Cadmium ion · metal · 2 copies · chains A, C, B, F, G

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Interfaces

21 interfaces between chains.

• A–B · 3196 Ų buried · 38 hydrogen bonds · protein-protein
• B–C · 1293 Ų buried · 11 hydrogen bonds · protein-protein
• B–G · 933 Ų buried · 1 hydrogen bond · protein-protein
• C–H · 842 Ų buried · 7 hydrogen bonds · protein-protein
• A–G · 761 Ų buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 2 cofactor, 2 disulfide, 1 covalent (heme attachment, disulfide, covalent ligand).

Compared structures

• 2E75 · Crystal Structure of the Cytochrome b6f Complex with 2-nonyl-4-hydroxyquinoline N-oxide… · the same entry in another collection · chain E against E, TM-score 1.00
• P83791 · AlphaFold monomer V2.0 prediction for cytochrome B6 (P83791) · a predicted model of the same protein · chain A against A, TM-score 0.99
• P83793 · AlphaFold monomer V2.0 prediction for cytochrome F (P83793) · a predicted model of the same protein · chain C against A, TM-score 0.98
• P83792 · AlphaFold monomer V2.0 prediction for cytochrome B6-F complex subunit 4 (P83792) · a predicted model of the same protein · chain B against A, TM-score 0.98
• P83794 · AlphaFold monomer V2.0 prediction for cytochrome B6-F complex iron- sulfur subunit… · a predicted model of the same protein · chain D against A, TM-score 0.94

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 P83791
• Every structure of UniProt P83792
• Every structure of UniProt P83793
• Every structure of UniProt P83794
• Every structure of UniProt P83795
• Every structure of UniProt P83796
• Every structure of UniProt P83797
• Every structure of UniProt P83798
• Elsewhere: RCSB PDB 2E75 · PDBe 2E75 · UniProt P83791 · UniProt P83792 · UniProt P83793 · UniProt P83794 · UniProt P83795 · UniProt P83796 · UniProt P83797 · UniProt P83798