Research workbench
3.15 ångström cryo-EM structure of the dimeric cytochrome B6F complex from synechocystis sp. pcc 6803 with natively bound plastoquinone and lipid molecules.
Analyse 3.15 ångström cryo-EM structure of the dimeric cytochrome B6F complex from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ZXY
- Type
- protein
- Length
- 1,913 residues
- Chains
- 16
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome B6; Cytochrome B6-F complex subunit 4; Cytochrome F; Cytochrome B6-F complex…
- EC
- 7.1.1.6
- UniProt
- Q57038, P27589, P26287, P26290, A0A6P1VG96, P74810, P74149, P72717
- Ligands
- PGV, HEM, HEC, ECH, CLA, LFA, FES
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 10 distinct chains · 46% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, I | Cytochrome B6 | protein | 220 | 70% helix, 1% strand | Q57038 |
| B | Cytochrome B6-F complex subunit 4 | protein | 158 | 51% helix, 3% strand | P27589 |
| C, K | Cytochrome F | protein | 279 | 19% helix, 28% strand | P26287 |
| D, L | Cytochrome B6-F complex iron-sulfur subunit 2 (EC 7.1.1.6) | protein | 168 | 22% helix, 25% strand | P26290 |
| E, M | Cytochrome B6 | protein | 32 | 81% helix, 0% strand | A0A6P1VG96 |
| F | Cytochrome B6-F complex subunit 7 | protein | 36 | 67% helix, 0% strand | P74810 |
| G, O | Cytochrome B6-F complex subunit 5 | protein | 35 | 74% helix, 0% strand | P74149 |
| H, P | Cytochrome B6-F complex subunit 8 | protein | 29 | 76% helix, 0% strand | P72717 |
| J | Cytochrome B6-F complex subunit 4 | protein | 159 | 54% helix, 3% strand | P27589 |
| N | Cytochrome B6-F complex subunit 7 | protein | 34 | 74% helix, 0% strand | P74810 |
Ligands and binding sites
- PGV · (1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11E)-octadec-11-enoate · ligand · 7 copies · chains A, B, F, G, C, D, I, J, K, L, O, N
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, I, J
- HEC · Heme C · ligand · 4 copies · chains A, B, H, C, I, J, P, K
- ECH · beta,beta-caroten-4-one · ligand · 2 copies · chains A, B, F, G, H, I, J, N, O, P
- CLA · Chlorophyll A · ligand · 2 copies · chains A, B, I, J
- LFA · Eicosane · ligand · 2 copies · chains E
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains D, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 363 | 0.86 | 0.94 | 45 | ECH |
| 2 | 1146 | 0.86 | 0.86 | 106 | HEM, HEC, CLA |
| 3 | 1154 | 0.86 | 0.86 | 100 | HEM, HEC, CLA |
| 4 | 956 | 0.85 | 0.86 | 115 | HEM |
| 5 | 277 | 0.84 | 0.95 | 45 | HEM |
Interfaces
52 interfaces between chains.
- A–B · 3445 Ų buried · 41 hydrogen bonds · protein-protein
- I–J · 3399 Ų buried · 34 hydrogen bonds · protein-protein
- A–I · 1780 Ų buried · 10 hydrogen bonds · protein-protein
- J–K · 1341 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1311 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 cofactor, 1 disulfide (heme c attachment, disulfide).
Compared structures
- 7ZXY · 3.15 Angstrom cryo-EM structure of the dimeric cytochrome b6f complex from Synechocystis… · 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 Q57038
- Every structure of UniProt P27589
- Every structure of UniProt P26287
- Every structure of UniProt P26290
- Every structure of UniProt A0A6P1VG96
- Every structure of UniProt P74810
- Every structure of UniProt P74149
- Every structure of UniProt P72717
- Elsewhere: RCSB PDB 7ZXY · PDBe 7ZXY · UniProt Q57038 · UniProt P27589 · UniProt P26287 · UniProt P26290 · UniProt A0A6P1VG96 · UniProt P74810 · UniProt P74149 · UniProt P72717
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