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Photosynthetic reaction center from rhodopseudomonas viridis (ubiquinone-2 complex)

Analyse Photosynthetic reaction center from rhodopseudomonas viridis (ubiquinone-2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2PRC
Type: protein
Length: 1,186 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Photosynthetic reaction center
UniProt: P07173, P06009, P06010, P06008
Ligands: HEM, BCB, BPB, UQ2, MQ7, NS5, FE2, SO4
Pockets: 17 · best druggability 0.89

Structure

x-ray diffraction · 4 distinct chains · 49% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Photosynthetic reaction center	protein	332	43% helix, 4% strand	P07173
L	Photosynthetic reaction center	protein	273	67% helix, 4% strand	P06009
M	Photosynthetic reaction center	protein	323	62% helix, 5% strand	P06010
H	Photosynthetic reaction center	protein	258	24% helix, 23% strand	P06008

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains C, L, M
BCB · Bacteriochlorophyll B · ligand · 4 copies · chains L, M
BPB · Bacteriopheophytin B · ligand · 2 copies · chains L, M
UQ2 · Ubiquinone-2 · ligand · chains L
MQ7 · Menaquinone-7 · ligand · chains L, M
NS5 · 15-cis-1,2-dihydroneurosporene · ligand · chains M
FE2 · Fe (II) ion · metal · chains L, M
SO4 · Sulfate ion · ion · 4 copies · chains L, M, H
LDA · Lauryl dimethylamine-N-oxide · additive · 6 copies · chains L, M, H

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	822	0.89	0.91	103	HEM
2	1079	0.83	0.83	86	BCB, BPB
3	88	0.76	0.98	33	empty
4	311	0.74	0.86	38	MQ7
5	57	0.72	0.99	24	empty

Interfaces

6 interfaces between chains.

L–M · 4393 Å² buried · 61 hydrogen bonds · protein-protein
M–H · 2874 Å² buried · 46 hydrogen bonds · protein-protein
C–M · 2749 Å² buried · 34 hydrogen bonds · protein-protein
L–H · 1926 Å² buried · 28 hydrogen bonds · protein-protein
C–L · 1798 Å² buried · 30 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 cofactor, 1 modified (heme attachment, formylation).

Compared structures

2PRC · Photosynthetic reaction center from rhodopseudomonas viridis (ubiquinone-2 complex) · the same entry in another collection · chain H against H, TM-score 1.00
P07173 · AlphaFold monomer V2.0 prediction for photosynthetic reaction center cytochrome C subunit… · a predicted model of the same protein · chain C against A, TM-score 1.00
P06009 · AlphaFold monomer V2.0 prediction for reaction center protein L chain (P06009) · a predicted model of the same protein · chain L against A, TM-score 0.99
P06010 · AlphaFold monomer V2.0 prediction for reaction center protein M chain (P06010) · a predicted model of the same protein · chain M against A, TM-score 0.97
P06008 · AlphaFold monomer V2.0 prediction for reaction center protein H chain (P06008) · a predicted model of the same protein · chain H 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 P07173
Every structure of UniProt P06009
Every structure of UniProt P06010
Every structure of UniProt P06008
Elsewhere: RCSB PDB 2PRC · PDBe 2PRC · UniProt P07173 · UniProt P06009 · UniProt P06010 · UniProt P06008

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