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Structure of photosynthetic LH1-rc super-complex of rhodobacter sphaeroides lacking protein-U

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: 7VY3
Type: protein
Length: 1,846 residues
Chains: 25
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Photosynthetic reaction center L subunit; Reaction center protein M chain; Photosynthetic…
UniProt: A0A7Z6QV46, A0A7Z6QV86, A0A7Z6QV87, A0A7Z6W8S0, A0A7Z6QV72, A0A7Z6QV32
Ligands: BCL, SPO, PGV, U10, CDL, BPH, PTY, 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, 5% strand	A0A7Z6QV46
M	Reaction center protein M chain	protein	306	61% helix, 4% strand	A0A7Z6QV86
H	Photosynthetic reaction center subunit H	protein	246	23% helix, 24% strand	A0A7Z6QV87
A	Antenna pigment protein alpha chain	protein	45	69% helix, 0% strand	A0A7Z6W8S0
B	Antenna pigment protein beta chain	protein	44	73% helix, 0% strand	A0A7Z6QV72
D, F, I, K, O, Q, S	Antenna pigment protein alpha chain	protein	54	72% helix, 0% strand	A0A7Z6W8S0
E, J, N, P, R, T	Antenna pigment protein beta chain	protein	43	74% helix, 0% strand	A0A7Z6QV72
G	Antenna pigment protein beta chain	protein	45	71% helix, 0% strand	A0A7Z6QV72
V	Antenna pigment protein alpha chain	protein	52	79% helix, 0% strand	A0A7Z6W8S0
W	Antenna pigment protein beta chain	protein	42	76% helix, 0% strand	A0A7Z6QV72
Y	Antenna pigment protein alpha chain	protein	39	82% helix, 0% strand	A0A7Z6W8S0
Z	Antenna pigment protein beta chain	protein	31	84% helix, 0% strand	A0A7Z6QV72
1	Antenna pigment protein alpha chain	protein	27	93% helix, 0% strand	A0A7Z6W8S0
X	Pufx	protein	52	71% helix, 0% strand	A0A7Z6QV32

Ligands and binding sites

BCL · Bacteriochlorophyll A · ligand · 25 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
SPO · Spheroidene · ligand · 19 copies · chains M, S, V, A, B, D, X, E, F, G, I, J, K, N, O, P, Q, R, T, W, Y, Z, 1
PGV · (1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11E)-octadec-11-enoate · ligand · 8 copies · chains L, I, M, S, V, H, F, D, K, O, Q, Y, 1
U10 · Ubiquinone-10 · ligand · 4 copies · chains L, M, D, F, A, B, E, X
CDL · Cardiolipin · ligand · 3 copies · chains L, M, H, I, K, O, V, Y
BPH · Bacteriopheophytin A · ligand · 2 copies · chains L, M
PTY · Phosphatidylethanolamine · ligand · 2 copies · chains L, M, H, F
FE · Fe (III) ion · metal · chains L, M
LMT · Dodecyl-beta-D-maltoside · additive · 17 copies · chains L, M, X, H, Q, S, K, O, A, D, B, E, G, F, J, I, N
LDA · Lauryl dimethylamine-N-oxide · additive · 4 copies · chains L, M, H, Y, A, X

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	990	0.85	0.85	93	SPO, PGV
2	1144	0.84	0.84	91	LMT, SPO, U10, LDA
3	807	0.82	0.85	72	BCL
4	633	0.80	0.84	77	PGV
5	111	0.78	0.97	32	empty

Interfaces

69 interfaces between chains.

L–M · 4768 Å² buried · 72 hydrogen bonds · protein-protein
M–H · 2922 Å² buried · 47 hydrogen bonds · protein-protein
L–H · 1599 Å² buried · 13 hydrogen bonds · protein-protein
L–X · 943 Å² buried · 4 hydrogen bonds · protein-protein
O–P · 820 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified (formylation).

Compared structures

7VY3 · Structure of photosynthetic LH1-rc super-complex of rhodobacter sphaeroides lacking… · the same entry in another collection · chain M against M, 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 A0A7Z6QV46
Every structure of UniProt A0A7Z6QV86
Every structure of UniProt A0A7Z6QV87
Every structure of UniProt A0A7Z6W8S0
Every structure of UniProt A0A7Z6QV72
Every structure of UniProt A0A7Z6QV32
Elsewhere: RCSB PDB 7VY3 · PDBe 7VY3 · UniProt A0A7Z6QV46 · UniProt A0A7Z6QV86 · UniProt A0A7Z6QV87 · UniProt A0A7Z6W8S0 · UniProt A0A7Z6QV72 · UniProt A0A7Z6QV32

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