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Crystallographic refinement at 2.3 ångströms resolution and refined model of the photosynthetic reaction center from rhodopseudomonas viridis

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PDB: 1PRC
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: HEC, BCB, BPB, UQ1, MQ7, NS1, FE, SO4
Pockets: 18 · best druggability 0.88

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	42% helix, 3% strand	P07173
L	Photosynthetic reaction center	protein	273	64% helix, 4% strand	P06009
M	Photosynthetic reaction center	protein	323	62% helix, 5% strand	P06010
H	Photosynthetic reaction center	protein	258	23% helix, 24% strand	P06008

Ligands and binding sites

HEC · Heme C · 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
UQ1 · Ubiquinone-1 · ligand · chains L, M
MQ7 · Menaquinone-7 · ligand · chains L, M
NS1 · 15-trans-1,2-dihydroneurosporene · ligand · chains M
FE · Fe (III) ion · metal · chains L, M
SO4 · Sulfate ion · ion · 7 copies · chains L, M, H
LDA · Lauryl dimethylamine-N-oxide · additive · 2 copies · chains M, H, L

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

Pockets

18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	998	0.88	0.88	128	HEC
2	1096	0.83	0.84	82	BCB, BPB
3	347	0.77	0.87	56	BPB, MQ7
4	101	0.77	0.97	30	empty
5	56	0.73	0.99	18	empty

Interfaces

6 interfaces between chains.

L–M · 4417 Å² buried · 59 hydrogen bonds · protein-protein
M–H · 2922 Å² buried · 47 hydrogen bonds · protein-protein
C–M · 2722 Å² buried · 31 hydrogen bonds · protein-protein
L–H · 1911 Å² buried · 29 hydrogen bonds · protein-protein
C–L · 1785 Å² buried · 27 hydrogen bonds · protein-protein

Modifications

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

Compared structures

1PRC · Crystallographic refinement at 2.3 ångströms resolution and refined model of the… · 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 0.93

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 1PRC · PDBe 1PRC · UniProt P07173 · UniProt P06009 · UniProt P06010 · UniProt P06008

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