MolNFT v1 · #186126 · protein
2.8 ångström cryo-EM structure of the dimeric cytochrome B6F-petp complex from synechocystis sp. pcc 6803 with natively bound lipids and plastoquinone molecules
7R0W · Uncharacterized protein CP097, conserved in cyanobacteria: “2.8 ångström cryo-EM structure of the dimeric cytochrome B6F-petp complex from synechocystis sp. pcc 6803…”. Electron microscopy, 12 ligands (HEM, PGV, ECH), 20 pockets…
- PDB
- 7R0W
- Type
- protein
- Length
- 2,040 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein CP097, conserved in cyanobacteria; Cytochrome B6; Cytochrome B6-F…
- UniProt
- A0A068MZK2, Q57038, P27589, P26287, A0A6P1VG96, P74810, P74149, P72717
- Ligands
- HEM, PGV, ECH, PL9, CLA, HEC, 6PL, FES, SQD, LMG, 2WA, LFA
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 9 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X, V | Uncharacterized protein CP097, conserved in cyanobacteria | protein | 64 | 14% helix, 38% strand | A0A068MZK2 |
| I, A | Cytochrome B6 | protein | 222 | 75% helix, 1% strand | Q57038 |
| J, B | Cytochrome B6-F complex subunit 4 | protein | 159 | 61% helix, 4% strand | P27589 |
| K, C | Cytochrome F | protein | 279 | 20% helix, 28% strand | P26287 |
| M, E | Cytochrome B6 | protein | 32 | 84% helix, 0% strand | A0A6P1VG96 |
| N, F | Cytochrome B6-F complex subunit 7 | protein | 34 | 85% helix, 3% strand | P74810 |
| O, G | Cytochrome B6-F complex subunit 5 | protein | 32 | 81% helix, 0% strand | P74149 |
| P, H | Cytochrome B6-F complex subunit 8 | protein | 29 | 83% helix, 0% strand | P72717 |
| D, L | Rieske domain, petc | protein | 169 | 22% helix, 16% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 6 copies · chains I, J, A, P, B, H
- PGV · (1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11E)-octadec-11-enoate · ligand · 4 copies · chains I, J, K, L, A, B, C, D
- ECH · beta,beta-caroten-4-one · ligand · 2 copies · chains I, J, N, O, P, A, B, F, G, H
- PL9 · 2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2, 6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone · ligand · 2 copies · chains I, J, A, B, D
- CLA · Chlorophyll A · ligand · 2 copies · chains I, J, A, B
- HEC · Heme C · ligand · 2 copies · chains K, C
- 6PL · (4S,7R)-4-hydroxy-N,N,N-trimethyl-9-oxo-7-[(palmitoyloxy)methyl]-3,5,8-trioxa-4-phosphahexacosan-1-aminium 4-oxide · ligand · 2 copies · chains I, J, K, M, N, O, P, A, B, C, E, F, G, H
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains D, L
- SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · 2 copies · chains A, B, C, D, I, J, K, L
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · chains I, J, N, O
- 2WA · (1S,8E)-1-{[(2S)-1-hydroxy-3-{[(1S)-1-hydroxypentadecyl]oxy}propan-2-yl]oxy}heptadec-8-en-1-ol · ligand · chains A, B, F, G
- LFA · Eicosane · ligand · chains C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 852 | 0.87 | 0.88 | 84 | HEM, CLA |
| 2 | 1097 | 0.86 | 0.87 | 104 | HEM, CLA |
| 3 | 1039 | 0.85 | 0.86 | 133 | HEM |
| 4 | 539 | 0.85 | 0.90 | 60 | ECH, 6PL |
| 5 | 1088 | 0.84 | 0.85 | 130 | HEM |
Interfaces
57 interfaces between chains.
- A–B · 3279 Ų buried · 35 hydrogen bonds · protein-protein
- I–J · 3278 Ų buried · 32 hydrogen bonds · protein-protein
- I–A · 1789 Ų buried · 16 hydrogen bonds · protein-protein
- J–K · 1300 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1279 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor, 2 disulfide (heme c attachment, disulfide).
Compared structures
- 7R0W · 2.8 Angstrom cryo-EM structure of the dimeric cytochrome b6f-PetP complex from… · the same entry in another collection · chain C against C, 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 A0A068MZK2
- Every structure of UniProt Q57038
- Every structure of UniProt P27589
- Every structure of UniProt P26287
- Every structure of UniProt A0A6P1VG96
- Every structure of UniProt P74810
- Every structure of UniProt P74149
- Every structure of UniProt P72717
- Elsewhere: RCSB PDB 7R0W · PDBe 7R0W · UniProt A0A068MZK2 · UniProt Q57038 · UniProt P27589 · UniProt P26287 · UniProt A0A6P1VG96 · UniProt P74810 · UniProt P74149 · UniProt P72717
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