MolNFT v1 · #35298 · protein
Crystal structure of the cytochrome B6F complex with tridecyl- stigmatellin (tds) from M.LAMINOSUS
2E76: “Crystal structure of the cytochrome B6F complex with tridecyl- stigmatellin (tds) from M.LAMINOSUS”. X-ray diffraction, 9 ligands (HEM, UMQ, OPC), 9 pockets (best druggability 0.86). MolNFT v1 #35298 on GenesisL1: 3D structure…
- PDB
- 2E76
- Type
- protein
- Length
- 961 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
- 1.10.99.1
- UniProt
- P83791, P83792, P83793, P83794, P83795, P83796, P83797, P83798
- Ligands
- HEM, UMQ, OPC, TDS, CLA, FES, SQD, BCR, CD
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 8 distinct chains · 45% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome B6 | protein | 215 | 73% helix, 1% strand | P83791 |
| B | Cytochrome B6-F complex subunit 4 | protein | 160 | 51% helix, 2% strand | P83792 |
| C | Apocytochrome F | protein | 288 | 18% helix, 21% strand | P83793 |
| D | Cytochrome B6-F complex iron-sulfur subunit (EC 1.10.99.1) | protein | 168 | 22% helix, 18% strand | P83794 |
| E | Cytochrome B6-F complex subunit 6 | protein | 32 | 81% helix, 0% strand | P83795 |
| F | Cytochrome B6-F complex subunit 7 | protein | 32 | 81% helix, 0% strand | P83796 |
| G | Cytochrome B6-F complex subunit 5 | protein | 37 | 65% helix, 0% strand | P83797 |
| H | Cytochrome B6-F complex subunit 8 | protein | 29 | 83% 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 · 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
- TDS · 8-hydroxy-5,7-dimethoxy-3-methyl-2-tridecyl-4H-chromen-4-one · ligand · 2 copies · 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 · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 638 | 0.86 | 0.91 | 78 | HEM |
| 2 | 1167 | 0.86 | 0.86 | 114 | HEM, CLA, TDS |
| 3 | 516 | 0.86 | 0.91 | 53 | OPC, BCR |
| 4 | 188 | 0.68 | 0.86 | 36 | HEM |
| 5 | 530 | 0.67 | 0.77 | 62 | empty |
Interfaces
21 interfaces between chains.
- A–B · 3092 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 1292 Ų buried · 11 hydrogen bonds · protein-protein
- B–G · 930 Ų buried · 4 hydrogen bonds · protein-protein
- C–H · 811 Ų buried · 6 hydrogen bonds · protein-protein
- A–G · 726 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 cofactor (disulfide, heme attachment).
Compared structures
- 2E76 · Crystal Structure of the Cytochrome b6f Complex with tridecyl-stigmatellin (TDS) from… · 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 0.82
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 2E76 · PDBe 2E76 · UniProt P83791 · UniProt P83792 · UniProt P83793 · UniProt P83794 · UniProt P83795 · UniProt P83796 · UniProt P83797 · UniProt P83798
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