MolNFT v1 · #102267 · protein
Internal lipid architecture of the hetero-oligomeric cytochrome B6F complex
4OGQ: “Internal lipid architecture of the hetero-oligomeric cytochrome B6F complex”. X-ray diffraction, 16 ligands (UMQ, 7PH, HEC), 9 pockets (best druggability 0.86). MolNFT v1 #102267 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4OGQ
- Type
- protein
- Length
- 949 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
- 1.10.9.1
- UniProt
- P0A384, Q93SX1, Q93SW9, Q93SX0, Q8YVQ2, P0A3Y1, P58246, P61048
- Ligands
- UMQ, 7PH, HEC, 8K6, 2WM, CLA, OPC, MYS, SQD, FES, 2WD, 3WM, 2WA, 1O2, BCR, CD
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 8 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome B6 | protein | 214 | 72% helix, 1% strand | P0A384 |
| B | Cytochrome B6-F complex subunit 4 | protein | 159 | 58% helix, 3% strand | Q93SX1 |
| C | Apocytochrome F | protein | 281 | 21% helix, 28% strand | Q93SW9 |
| D | Cytochrome B6-F complex iron-sulfur subunit 1 (EC 1.10.9.1) | protein | 166 | 21% helix, 24% strand | Q93SX0 |
| E | Cytochrome B6-F complex subunit 6 | protein | 31 | 84% helix, 0% strand | Q8YVQ2 |
| F | Cytochrome B6-F complex subunit 7 | protein | 32 | 88% helix, 0% strand | P0A3Y1 |
| G | Cytochrome B6-F complex subunit 5 | protein | 37 | 73% helix, 0% strand | P58246 |
| H | Cytochrome B6-F complex subunit 8 | protein | 29 | 83% helix, 0% strand | P61048 |
Ligands and binding sites
- UMQ · Undecyl-maltoside · ligand · 5 copies · chains A, B, C, D, E, G
- 7PH · (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate · ligand · 5 copies · chains A, B, G, C, E, H, D, F
- HEC · Heme C · ligand · 4 copies · chains A, B, H, C
- 8K6 · Octadecane · ligand · 4 copies · chains A, B, D
- 2WM · (1S,8E)-1-{[(2S)-3-hydroxy-2-{[(1S)-1-hydroxyoctadecyl]oxy}propyl]oxy}octadec-8-en-1-ol · ligand · chains A, B, D
- CLA · Chlorophyll A · ligand · chains A, B
- 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 · chains A, B
- MYS · Pentadecane · ligand · chains A, D
- SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · chains B, C, D
- FES · Fe2/s2 (inorganic) cluster · ligand · chains D
- 2WD · (1R)-1-{[(2S)-3-hydroxy-2-{[(1R)-1-hydroxypentyl]oxy}propyl]oxy}hexan-1-ol · ligand · chains D
- 3WM · (1S,8E,1'R,8'Z)-1,1'-{[(2S)-3-hydroxypropane-1,2-diyl]bis(oxy)}bisoctadec-8-en-1-ol · ligand · chains A, B, C, E, F, G, H
- 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
- 1O2 · (2S)-3-(alpha-D-galactopyranosyloxy)-2-(hexadecanoyloxy)propyl (9Z)-octadec-9-enoate · ligand · chains E, F
- BCR · Beta-carotene · ligand · chains A, B, F, G, H
- CD · Cadmium ion · metal · chains A, C
- OCT · N-octane · additive · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1196 | 0.86 | 0.86 | 114 | HEC, CLA, 2WA |
| 2 | 757 | 0.82 | 0.85 | 71 | 3WM, BCR |
| 3 | 1156 | 0.81 | 0.82 | 112 | HEC |
| 4 | 195 | 0.71 | 0.88 | 38 | HEC |
| 5 | 462 | 0.64 | 0.77 | 48 | CD, 7PH |
Interfaces
21 interfaces between chains.
- A–B · 3182 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 1322 Ų buried · 13 hydrogen bonds · protein-protein
- B–G · 950 Ų buried · 1 hydrogen bond · protein-protein
- A–G · 841 Ų buried · 2 hydrogen bonds · protein-protein
- C–H · 756 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 cofactor, 1 disulfide (heme c attachment, disulfide).
Compared structures
- 4OGQ · Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome b6f Complex · the same entry in another collection · chain H against H, TM-score 1.00
- Q93SW9 · AlphaFold monomer V2.0 prediction for cytochrome F (Q93SW9) · a predicted model of the same protein · chain C against A, TM-score 0.99
- P0A384 · AlphaFold monomer V2.0 prediction for cytochrome B6 (P0A384) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q93SX1 · AlphaFold monomer V2.0 prediction for cytochrome B6-F complex subunit 4 (Q93SX1) · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q93SX0 · AlphaFold monomer V2.0 prediction for cytochrome B6-F complex iron- sulfur subunit 1… · 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 P0A384
- Every structure of UniProt Q93SX1
- Every structure of UniProt Q93SW9
- Every structure of UniProt Q93SX0
- Every structure of UniProt Q8YVQ2
- Every structure of UniProt P0A3Y1
- Every structure of UniProt P58246
- Every structure of UniProt P61048
- Elsewhere: RCSB PDB 4OGQ · PDBe 4OGQ · UniProt P0A384 · UniProt Q93SX1 · UniProt Q93SW9 · UniProt Q93SX0 · UniProt Q8YVQ2 · UniProt P0A3Y1 · UniProt P58246 · UniProt P61048
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