MolNFT v2 · #223709 · protein

Structure of PSII-FCPII-G/H complex in the PSII-FCPII supercomplex from Cyclotella meneghiniana

8W4O · FCPII-G, Fucoxanthin chlorophyll a/c binding protein: “Structure of PSII-FCPII-G/H complex in the PSII-FCPII supercomplex from Cyclotella meneghiniana”. Electron microscopy at 3.23, 7 ligands (CLA, A86, DD6), 9 pockets (best…

PDB: 8W4O
Type: protein
Length: 497 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.23
Source: Stephanocyclus meneghinianus
Molecule: FCPII-G, Fucoxanthin chlorophyll a/c binding protein; FCPII-H2, Fucoxanthin chlorophyll…
Ligands: CLA, A86, DD6, LHG, ET4, LMG, SQD
Pockets: 9 · best druggability 0.61

Structure

electron microscopy · resolution 3.23 · 3 distinct chains · 51% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
5	FCPII-G, Fucoxanthin chlorophyll a/c binding protein	protein	169	57% helix, 0% strand	—
7	FCPII-H2, Fucoxanthin chlorophyll a/c binding protein	protein	164	46% helix, 0% strand	—
6	FCPII-H1, Fucoxanthin chlorophyll a/c binding protein	protein	164	49% helix, 0% strand	—

Ligands and binding sites

CLA · Chlorophyll A · ligand · 36 copies · chains 5, 6, 7
A86 · (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate · ligand · 6 copies · chains 5, 6, 7
DD6 · (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol · ligand · 4 copies · chains 7, 6
LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 3 copies · chains 5
ET4 · (1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15-octaen-17-ynyl]cyclohex-3-en-1-ol · ligand · chains 5
LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · chains 5
SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · chains 5, 6

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	481	0.61	0.75	48	CLA
2	243	0.58	0.79	27	CLA
3	258	0.55	0.76	25	CLA
4	293	0.53	0.74	24	CLA
5	220	0.52	0.76	25	CLA

Interfaces

2 interfaces between chains.

7–6 · 393 Å² buried · 0 hydrogen bonds · protein-protein
5–6 · 290 Å² buried · 4 hydrogen bonds · protein-protein

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 8W4O · PDBe 8W4O

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