Research workbench

Structure of photosynthetic LH1-rc super-complex of rhodobacter sphaeroides monomer

Analyse Structure of photosynthetic LH1-rc super-complex of rhodobacter sphaeroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7F0L
Type: protein
Length: 2,277 residues
Chains: 33
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Photosynthetic reaction center L subunit; Reaction center protein M chain; Reaction…
UniProt: Q7B300, P0C0X9, A0A330HGC2, A0A3G6WQU3
Ligands: BCL, SPO, PGV, CDL, U10, BPH, FE
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 14 distinct chains · 59% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Photosynthetic reaction center L subunit	protein	281	62% helix, 4% strand	—
M	Reaction center protein M chain	protein	306	61% helix, 5% strand	—
H	Reaction center protein H chain	protein	246	22% helix, 26% strand	—
A	Light-harvesting protein B-875 alpha chain	protein	45	69% helix, 0% strand	—
B	Antenna pigment protein beta chain	protein	44	73% helix, 0% strand	Q7B300
D, F, I, K, O, Q, S, V, Y, 1, 3	Light-harvesting protein B-875 alpha chain	protein	54	78% helix, 0% strand	—
E, J, N, P, R, T, W, Z, 4	Antenna pigment protein beta chain	protein	43	74% helix, 0% strand	Q7B300
G	Antenna pigment protein beta chain	protein	45	71% helix, 0% strand	Q7B300
2, 6	Antenna pigment protein beta chain	protein	42	76% helix, 0% strand	Q7B300
5	Light-harvesting protein B-875 alpha chain	protein	53	74% helix, 0% strand	P0C0X9
7	Light-harvesting protein B-875 alpha chain	protein	51	73% helix, 0% strand	P0C0X9
8	Antenna pigment protein beta chain	protein	38	84% helix, 0% strand	Q7B300
X	Pufx	protein	53	68% helix, 0% strand	A0A330HGC2
U	Protein-U	protein	50	80% helix, 0% strand	A0A3G6WQU3

Ligands and binding sites

BCL · Bacteriochlorophyll A · ligand · 32 copies · chains L, M, A, B, X, D, E, F, G, I, J, K, N, O, P, Q, R, S, T, V, W, Y, Z, 1, 2, 3, 4, 5, 6, 7, 8
SPO · Spheroidene · ligand · 27 copies · chains M, S, V, A, B, D, E, F, G, I, J, K, N, O, P, Q, R, T, W, Y, Z, 1, 2, 3, 4, 5, 6, 7, 8, X
PGV · (1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11E)-octadec-11-enoate · ligand · 13 copies · chains L, I, U, M, H, F, S, V, D, K, O, Q, Y, 1, 3, X
CDL · Cardiolipin · ligand · 4 copies · chains L, M, H, I, K, O, V, Y
U10 · Ubiquinone-10 · ligand · 3 copies · chains L, M, D
BPH · Bacteriopheophytin A · ligand · 2 copies · chains L, M
FE · Fe (III) ion · metal · chains L, M
LMT · Dodecyl-beta-D-maltoside · additive · 24 copies · chains M, H, U, L, K, O, Q, A, D, B, E, G, F, I, J, S, 1, 2, 4, 3, 5, X
LDA · Lauryl dimethylamine-N-oxide · additive · 6 copies · chains L, X, M, H, Y, A

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	991	0.85	0.85	100	SPO, PGV, LMT
2	1107	0.84	0.84	89	LMT, SPO, LDA
3	1188	0.82	0.83	94	BCL, BPH
4	121	0.78	0.97	34	empty
5	1164	0.78	0.80	83	PGV, SPO

Interfaces

95 interfaces between chains.

L–M · 4786 Å² buried · 59 hydrogen bonds · protein-protein
M–H · 2926 Å² buried · 35 hydrogen bonds · protein-protein
L–H · 1599 Å² buried · 16 hydrogen bonds · protein-protein
L–X · 954 Å² buried · 4 hydrogen bonds · protein-protein
V–W · 847 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified (formylation).

Compared structures

7F0L · Structure of photosynthetic LH1-rc super-complex of rhodobacter sphaeroides monomer · the same entry in another collection · chain J against J, TM-score 1.00

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 Q7B300
Every structure of UniProt P0C0X9
Every structure of UniProt A0A330HGC2
Every structure of UniProt A0A3G6WQU3
Elsewhere: RCSB PDB 7F0L · PDBe 7F0L · UniProt Q7B300 · UniProt P0C0X9 · UniProt A0A330HGC2 · UniProt A0A3G6WQU3

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.