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Lipidic sponge phase crystal structure of the photosynthetic reaction centre from blastochloris viridis (low dose)

Analyse Lipidic sponge phase crystal structure of the photosynthetic reaction centre… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2WJM
Type: protein
Length: 1,171 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Photosynthetic reaction center cytochrome C subunit; Reaction center protein H chain…
UniProt: P07173, P06008, P06009, P06010
Ligands: HEC, BCB, MPG, BPB, DGA, MQ7, NS5, FE2, PO4
Pockets: 16 · best druggability 0.87

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	protein	332	43% helix, 4% strand	P07173
H	Reaction center protein H chain	protein	243	25% helix, 25% strand	P06008
L	Reaction center protein L chain	protein	273	64% helix, 4% strand	P06009
M	Reaction center protein M chain	protein	323	62% 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
MPG · [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate · ligand · 3 copies · chains L, M
BPB · Bacteriopheophytin B · ligand · 2 copies · chains L, M
DGA · Diacyl glycerol · ligand · chains C, L, M
MQ7 · Menaquinone-7 · ligand · chains L, M
NS5 · 15-cis-1,2-dihydroneurosporene · ligand · chains M
FE2 · Fe (II) ion · metal · chains L, M
PO4 · Phosphate ion · ion · 2 copies · chains M, H, L

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

Pockets

16 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	927	0.87	0.89	125	HEC
2	979	0.85	0.85	87	BCB
3	84	0.73	0.96	25	empty
4	185	0.73	0.89	30	MQ7
5	424	0.66	0.79	41	empty

Interfaces

6 interfaces between chains.

L–M · 4412 Å² buried · 62 hydrogen bonds · protein-protein
H–M · 2870 Å² buried · 46 hydrogen bonds · protein-protein
C–M · 2736 Å² buried · 34 hydrogen bonds · protein-protein
H–L · 1788 Å² buried · 23 hydrogen bonds · protein-protein
C–L · 1782 Å² buried · 30 hydrogen bonds · protein-protein

Modifications

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

Compared structures

2WJM · Lipidic sponge phase crystal structure of the photosynthetic reaction centre from… · 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 0.98
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 0.95

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 2WJM · PDBe 2WJM · UniProt P07173 · UniProt P06008 · UniProt P06009 · UniProt P06010

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