Research workbench

Photosynthetic reaction center from rhodopseudomonas viridis - his L168 phe mutant (terbutryn complex)

Analyse Photosynthetic reaction center from rhodopseudomonas viridis - his L168 phe… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1DXR
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; Photosynthetic reaction center H…
UniProt: P07173, P06008, P06009, P06010
Ligands: HEC, BCB, BPB, MQ9, MST, NS5, FE2, SO4
Pockets: 19 · best druggability 0.88

Structure

x-ray diffraction · 4 distinct chains · 50% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Photosynthetic reaction center cytochrome C subunit	protein	332	44% helix, 4% strand	P07173
H	Photosynthetic reaction center H subunit	protein	258	26% helix, 23% strand	P06008
L	Photosynthetic reaction center L subunit	protein	273	66% helix, 4% strand	P06009
M	Photosynthetic reaction center M subunit	protein	323	63% helix, 5% strand	P06010

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
MQ9 · Menaquinone-9 · ligand · chains L, M
MST · 2-T-butylamino-4-ethylamino-6-methylthio-S-triazine · 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 H, M, L
LDA · Lauryl dimethylamine-N-oxide · additive · 6 copies · chains H, M, L

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

Pockets

19 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	872	0.88	0.90	109	HEC
2	866	0.84	0.85	78	BCB
3	100	0.77	0.98	34	empty
4	347	0.77	0.87	54	BPB, MQ9
5	55	0.72	0.99	24	empty

Interfaces

6 interfaces between chains.

L–M · 4409 Å² buried · 62 hydrogen bonds · protein-protein
H–M · 2897 Å² buried · 44 hydrogen bonds · protein-protein
C–M · 2765 Å² buried · 35 hydrogen bonds · protein-protein
H–L · 1901 Å² buried · 23 hydrogen bonds · protein-protein
C–L · 1804 Å² buried · 29 hydrogen bonds · protein-protein

Modifications

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

Compared structures

1DXR · Photosynthetic reaction center from Rhodopseudomonas viridis - His L168 Phe mutant… · the same entry in another collection · chain M against M, 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 P06008
Every structure of UniProt P06009
Every structure of UniProt P06010
Elsewhere: RCSB PDB 1DXR · PDBe 1DXR · UniProt P07173 · UniProt P06008 · UniProt P06009 · UniProt P06010

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