Research workbench

Photosynthetic reaction center blastochloris viridis (atcc)

Analyse Photosynthetic reaction center blastochloris viridis (atcc) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1R2C
Type: protein
Length: 1,186 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Photosynthetic reaction center cytochrome C subunit precursor; Reaction center protein L…
UniProt: P06009, P07173, P06010, P06008
Ligands: HEM, BCB, BPB, MQ7, UQ2, NS5, FE2, SO4
Pockets: 15 · best druggability 0.85

Structure

x-ray diffraction · 4 distinct chains · 49% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Photosynthetic reaction center cytochrome C subunit precursor	protein	332	42% helix, 5% strand	P06009
L	Reaction center protein L chain	protein	273	66% helix, 3% strand	P07173
M	Reaction center protein M chain	protein	323	62% helix, 5% strand	P06010
H	Reaction center protein H chain	protein	258	25% helix, 24% 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
MQ7 · Menaquinone-7 · ligand · chains L, M
UQ2 · Ubiquinone-2 · ligand · chains L
NS5 · 15-cis-1,2-dihydroneurosporene · ligand · chains M
FE2 · Fe (II) ion · metal · chains L, M
SO4 · Sulfate ion · ion · 4 copies · chains M, H, L
LDA · Lauryl dimethylamine-N-oxide · additive · 6 copies · chains M, H, L

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

Pockets

15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1190	0.85	0.86	119	BCB, BPB, MQ7, LDA
2	598	0.85	0.90	77	HEM
3	309	0.77	0.88	46	HEM
4	78	0.73	0.97	26	empty
5	51	0.71	0.99	20	empty

Interfaces

6 interfaces between chains.

L–M · 4373 Å² buried · 61 hydrogen bonds · protein-protein
M–H · 2856 Å² buried · 46 hydrogen bonds · protein-protein
C–M · 2801 Å² buried · 35 hydrogen bonds · protein-protein
L–H · 1904 Å² buried · 20 hydrogen bonds · protein-protein
C–L · 1784 Å² buried · 30 hydrogen bonds · protein-protein

Modifications

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

Compared structures

1R2C · Photosynthetic reaction center blastochloris viridis (atcc) · the same entry in another collection · chain H against H, TM-score 1.00
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
P07173 · AlphaFold monomer V2.0 prediction for photosynthetic reaction center cytochrome C subunit… · a predicted model of the same protein · chain L against A, TM-score 0.31
P06009 · AlphaFold monomer V2.0 prediction for reaction center protein L chain (P06009) · a predicted model of the same protein · chain C against A, TM-score 0.28

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 P06009
Every structure of UniProt P07173
Every structure of UniProt P06010
Every structure of UniProt P06008
Elsewhere: RCSB PDB 1R2C · PDBe 1R2C · UniProt P06009 · UniProt P07173 · UniProt P06010 · UniProt P06008

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