Research workbench
Crystal structure of cytochrome B6F in dopg, with disordered rieske iron-sulfur protein soluble domain
Analyse Crystal structure of cytochrome B6F in dopg, with disordered rieske iron-sulfur… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4I7Z
- Type
- protein
- Length
- 820 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome B6; Cytochrome B6-F complex subunit 4; Apocytochrome F; Cytochrome B6-F…
- EC
- 1.10.9.1
- UniProt
- P83791, P83792, P83793, P83794, P83795, P83796, P83797, P83798
- Ligands
- HEM, UMQ, OZ2, MYS, 8K6, CLA, 1E2, BCR, CD
- Pockets
- 11 · best druggability 0.86
Structure
x-ray diffraction · 8 distinct chains · 53% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome B6 | protein | 213 | 73% helix, 1% strand | P83791 |
| B | Cytochrome B6-F complex subunit 4 | protein | 159 | 60% helix, 3% strand | P83792 |
| C | Apocytochrome F | protein | 288 | 19% helix, 25% strand | P83793 |
| D | Cytochrome B6-F complex iron-sulfur subunit (EC 1.10.9.1) | protein | 38 | 79% helix, 0% strand | P83794 |
| E | Cytochrome B6-F complex subunit 6 | protein | 28 | 89% helix, 0% strand | P83795 |
| F | Cytochrome B6-F complex subunit 7 | protein | 31 | 87% helix, 0% strand | P83796 |
| G | Cytochrome B6-F complex subunit 5 | protein | 35 | 77% helix, 0% strand | P83797 |
| H | Cytochrome B6-F complex subunit 8 | protein | 28 | 86% helix, 0% strand | P83798 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, H, C
- UMQ · Undecyl-maltoside · ligand · 3 copies · chains A, B, C
- OZ2 · (2R)-3-{[(R)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-2-[(6Z)-tridec-6-enoyloxy]propyl (9Z)-octadec-9-enoate · ligand · 3 copies · chains A, B, C, D, E, F, G, H
- MYS · Pentadecane · ligand · chains A
- 8K6 · Octadecane · ligand · chains A
- CLA · Chlorophyll A · ligand · chains A, B
- 1E2 · (2S)-3-(acetyloxy)-2-hydroxypropyl 6-deoxy-6-sulfo-beta-D-glucopyranoside · ligand · chains B, C, D
- BCR · Beta-carotene · ligand · chains A, B, F, G, H
- CD · Cadmium ion · metal · 3 copies · chains A, C, B, F, G
- OCT · N-octane · additive · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 792 | 0.86 | 0.88 | 82 | HEM, CLA |
| 2 | 555 | 0.85 | 0.90 | 55 | BCR, OZ2 |
| 3 | 1014 | 0.83 | 0.84 | 90 | HEM, CD |
| 4 | 209 | 0.71 | 0.88 | 40 | HEM |
| 5 | 87 | 0.67 | 0.92 | 27 | empty |
Interfaces
21 interfaces between chains.
- A–B · 3176 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1221 Ų buried · 10 hydrogen bonds · protein-protein
- B–G · 789 Ų buried · 2 hydrogen bonds · protein-protein
- A–G · 777 Ų buried · 1 hydrogen bond · protein-protein
- C–H · 733 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4I7Z · Crystal structure of cytochrome b6f in DOPG, with disordered Rieske Iron-Sulfur Protein… · the same entry in another collection · chain H against H, 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
- 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
- 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
- P83797 · AlphaFold monomer V2.0 prediction for cytochrome B6-F complex subunit 5 (P83797) · a predicted model of the same protein · chain G against A, TM-score 0.89
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 4I7Z · PDBe 4I7Z · UniProt P83791 · UniProt P83792 · UniProt P83793 · UniProt P83794 · UniProt P83795 · UniProt P83796 · UniProt P83797 · UniProt P83798
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