Research workbench
Cytochrome B6F structure from M. laminosus with the qui analog inhibitor stigmatellin
Analyse Cytochrome B6F structure from M. laminosus with the qui analog inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PV1
- Type
- protein
- Length
- 942 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3
- Source
- Mastigocladus laminosus
- 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
- HEC, UMQ, OPC, MYS, SMA, 7PH, 8K6, CLA, FES, SQD, BCR, CD
- Pockets
- 13 · best druggability 0.87
Structure
x-ray diffraction · resolution 3 · 8 distinct chains · 45% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome b6 | protein | 213 | 71% helix, 1% strand | P83791 |
| B | Cytochrome b6-f complex subunit 4 | protein | 159 | 51% helix, 4% strand | P83792 |
| C | Apocytochrome f | protein | 288 | 18% helix, 25% strand | P83793 |
| D | Cytochrome b6-f complex iron-sulfur subunit (EC 1.10.9.1) | protein | 158 | 23% helix, 17% 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 | 90% helix, 0% strand | P83796 |
| G | Cytochrome b6-f complex subunit 5 | protein | 37 | 73% helix, 0% strand | P83797 |
| H | Cytochrome b6-f complex subunit 8 | protein | 28 | 82% helix, 0% strand | P83798 |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains A, B, H, C
- UMQ · Undecyl-maltoside · ligand · 3 copies · chains A, B, C
- 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 · 3 copies · chains A, B, D, C, E, F, G, H
- MYS · Pentadecane · ligand · chains A
- SMA · Stigmatellin A · ligand · chains A, B, D
- 7PH · (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate · ligand · chains A, B, C, D
- 8K6 · Octadecane · ligand · chains A, B, D
- 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
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 919 | 0.87 | 0.88 | 104 | HEC, CLA |
| 2 | 535 | 0.86 | 0.91 | 55 | OPC, BCR |
| 3 | 462 | 0.83 | 0.90 | 55 | HEC |
| 4 | 231 | 0.72 | 0.88 | 40 | HEC |
| 5 | 286 | 0.69 | 0.84 | 46 | empty |
Interfaces
21 interfaces between chains.
- A–B · 3246 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 1223 Ų buried · 10 hydrogen bonds · protein-protein
- B–G · 926 Ų buried · 2 hydrogen bonds · protein-protein
- A–G · 817 Ų buried · 1 hydrogen bond · protein-protein
- C–H · 744 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor, 1 disulfide (heme c attachment, disulfide).
Compared structures
- 4PV1 · Cytochrome B6F structure from M. laminosus with the quinone analog inhibitor stigmatellin · 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 0.99
- 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
- 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 4PV1 · PDBe 4PV1 · UniProt P83791 · UniProt P83792 · UniProt P83793 · UniProt P83794 · UniProt P83795 · UniProt P83796 · UniProt P83797 · UniProt P83798
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