MolNFT v1 · #163020 · protein
3.6 ångström cryo-EM structure of the dimeric cytochrome B6F complex from spinacia oleracea with natively bound thylakoid lipids and plastoquinone molecules
6RQF: “3.6 ångström cryo-EM structure of the dimeric cytochrome B6F complex from spinacia oleracea with natively…”. Electron microscopy, 10 ligands (HEM, HEC, PGV), 20 pockets (best druggability 0.87). MolNFT v1 #163020 on GenesisL1: 3D…
- PDB
- 6RQF
- Type
- protein
- Length
- 1,944 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
- P00165, P00166, P16013, P08980, Q9M3L0, P80883, P69461, P61045
- Ligands
- HEM, HEC, PGV, PL9, 6PL, SQD, CLA, BCR, LMG, FES
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 8 distinct chains · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I, A | Cytochrome B6 | protein | 215 | 73% helix, 1% strand | P00165 |
| J, B | Cytochrome B6-F complex subunit 4 | protein | 160 | 49% helix, 3% strand | P00166 |
| K, C | Cytochrome F | protein | 285 | 18% helix, 29% strand | P16013 |
| L, D | Cytochrome B6-F complex iron-sulfur subunit, chloroplastic (EC 7.1.1.6) | protein | 179 | 21% helix, 25% strand | P08980 |
| M, E | Cytochrome B6-F complex subunit 6 | protein | 31 | 84% helix, 0% strand | Q9M3L0 |
| N, F | Cytochrome B6-F complex subunit 7 | protein | 36 | 86% helix, 0% strand | P80883 |
| O, G | Cytochrome B6-F complex subunit 5 | protein | 37 | 70% helix, 0% strand | P69461 |
| P, H | Cytochrome B6-F complex subunit 8 | protein | 29 | 79% helix, 0% strand | P61045 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains I, A, B
- HEC · Heme C · ligand · 4 copies · chains I, J, P, K, A, B, H, C
- 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
- 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 · 3 copies · chains I, J, A, L
- 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 · 3 copies · chains I, L, A, J, M, N, O, P, B, E, F, G, H
- SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · 3 copies · chains I, J, K, L, A, D, B, C
- CLA · Chlorophyll A · ligand · 2 copies · chains I, J, A, B
- BCR · Beta-carotene · ligand · 2 copies · chains I, J, N, O, P, A, B, F, G, H
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 2 copies · chains I, J, N, O, A, B, F, G
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains L, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 680 | 0.87 | 0.90 | 71 | HEM |
| 2 | 833 | 0.86 | 0.88 | 86 | HEM, HEC, CLA, LMG |
| 3 | 508 | 0.85 | 0.91 | 45 | BCR, 6PL |
| 4 | 1151 | 0.85 | 0.86 | 94 | HEM, HEC, CLA |
| 5 | 424 | 0.85 | 0.92 | 52 | HEM |
Interfaces
53 interfaces between chains.
- I–J · 3346 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 3294 Ų buried · 24 hydrogen bonds · protein-protein
- I–A · 1542 Ų buried · 12 hydrogen bonds · protein-protein
- J–K · 1413 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1368 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 cofactor, 2 disulfide (heme c attachment, disulfide).
Compared structures
- 6RQF · 3.6 Angstrom cryo-EM structure of the dimeric cytochrome b6f complex from Spinacia… · the same entry in another collection · chain B against B, 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 P00165
- Every structure of UniProt P00166
- Every structure of UniProt P16013
- Every structure of UniProt P08980
- Every structure of UniProt Q9M3L0
- Every structure of UniProt P80883
- Every structure of UniProt P69461
- Every structure of UniProt P61045
- Elsewhere: RCSB PDB 6RQF · PDBe 6RQF · UniProt P00165 · UniProt P00166 · UniProt P16013 · UniProt P08980 · UniProt Q9M3L0 · UniProt P80883 · UniProt P69461 · UniProt P61045
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