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Structure of photosynthetic LH1-rc super-complex of thiorhodovibrio strain 970

Analyse Structure of photosynthetic LH1-rc super-complex of thiorhodovibrio strain 970 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7C9R
Type: protein
Length: 3,009 residues
Chains: 36
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.82
Source: Thiorhodovibrio sp. 970
Molecule: Photosynthetic reaction center cytochrome c subunit; L subunit of the reaction center…
UniProt: H8Z3S2, G1BIY6, G1BIY7, H8Z0X5, G1BIY5, G1BIY9, G1BIY4, H8Z3S4, H8Z3R9, G1BIZ0
Ligands: BCL, PGV, H4X, HEM, CDL, BPH, UQ8, 8K6, DGA, MQ8, CA, MG, FE
Pockets: 20 · best druggability 0.90

Structure

electron microscopy · resolution 2.82 · 21 distinct chains · 54% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Photosynthetic reaction center cytochrome c subunit	protein	311	37% helix, 5% strand	H8Z3S2
L	L subunit of the reaction center	protein	272	62% helix, 3% strand	G1BIY6
M	Reaction center protein M chain	protein	318	59% helix, 4% strand	G1BIY7
H	Photosynthetic reaction center, subunit H, bacterial	protein	257	19% helix, 23% strand	H8Z0X5
A	Alpha subunit 1 of light-harvesting 1 complex	protein	70	63% helix, 0% strand	G1BIY5
B	Antenna complex alpha/beta subunit	protein	43	74% helix, 0% strand	G1BIY9
D, F, K	Alpha subunit 1 of light-harvesting 1 complex	protein	72	63% helix, 0% strand	G1BIY5
E, N, Z, 8	Antenna complex alpha/beta subunit	protein	42	76% helix, 0% strand	G1BIY4
G, J, X, 2, 0	Antenna complex alpha/beta subunit	protein	41	78% helix, 0% strand	G1BIY4
I, O	Alpha subunit 1 of light-harvesting 1 complex	protein	73	62% helix, 0% strand	G1BIY5
P	Antenna complex alpha/beta subunit	protein	42	76% helix, 0% strand	G1BIY9
Q	Antenna complex alpha/beta subunit	protein	78	38% helix, 0% strand	H8Z3S4
R	Antenna complex alpha/beta subunit	protein	44	73% helix, 0% strand	G1BIY4
S	LHC domain-containing protein	protein	72	63% helix, 0% strand	H8Z3R9
T, V, 6	Antenna complex alpha/beta subunit	protein	43	74% helix, 0% strand	G1BIY4
U, 1	LHC domain-containing protein	protein	72	69% helix, 0% strand	H8Z3R9
W, Y	LHC domain-containing protein	protein	73	62% helix, 0% strand	H8Z3R9
3, 7	LHC domain-containing protein	protein	73	64% helix, 0% strand	H8Z3R9
4	Antenna complex alpha/beta subunit	protein	44	73% helix, 0% strand	G1BIY9
5	LHC domain-containing protein	protein	74	69% helix, 0% strand	H8Z3R9
9	Alpha subunit 2 of light-harvesting 1 complex	protein	84	39% helix, 4% strand	G1BIZ0

Ligands and binding sites

BCL · Bacteriochlorophyll A · ligand · 36 copies · chains L, M, A, B, 9, 0, D, E, F, G, I, J, K, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, 1, 2, 3, 4, 5, 6, 7, 8
PGV · (1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11E)-octadec-11-enoate · ligand · 19 copies · chains C, M, H, L, K, O, Q, A, D, F, I, R, S, Y, 1, 3, 5, 7, 9
H4X · (6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E}, 22~{E},24~{E},26~{E})-2,31-dimethoxy-2,6,10,14,19,23, 27,31-octamethyl-dotriaconta-6,8,10,12,14,16,18,20,22, 24,26-undecaene · ligand · 17 copies · chains H, A, B, D, 9, E, F, G, I, J, K, N, O, M, Q, R, S, P, T, U, W, X, Y, V, Z, 1, 2, 3, 4, 5, 7, 8, 6, 0
HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains C, L, M
CDL · Cardiolipin · ligand · 3 copies · chains L, M, H, S, U, W, Y
BPH · Bacteriopheophytin A · ligand · 2 copies · chains L, M
UQ8 · Ubiquinone-8 · ligand · 2 copies · chains L, 5, 7
8K6 · Octadecane · ligand · 2 copies · chains L, 7, 9, 5
DGA · Diacyl glycerol · ligand · chains C, L
MQ8 · Menaquinone 8 · ligand · chains L, M, A, 9
CA · Calcium ion · metal · 17 copies · chains C, A, 0, B, D, E, F, G, I, J, K, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, 1, 2, 3, 4, 5, 6, 7, 8, 9
MG · Magnesium ion · metal · chains C, M
FE · Fe (III) ion · metal · chains L, M
LMT · Dodecyl-beta-D-maltoside · additive · 18 copies · chains A, B, D, E, 0, F, G, I, J, K, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, 1, 2, 3, 4, 5, 6, 7, 8, 9

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	1125	0.90	0.91	112	HEM
2	963	0.83	0.84	105	BCL
3	949	0.81	0.82	70	PGV, H4X
4	371	0.80	0.89	66	empty
5	970	0.79	0.80	77	H4X

Interfaces

120 interfaces between chains.

L–M · 4531 Å² buried · 51 hydrogen bonds · protein-protein
M–H · 2925 Å² buried · 30 hydrogen bonds · protein-protein
C–M · 2287 Å² buried · 19 hydrogen bonds · protein-protein
L–H · 1845 Å² buried · 16 hydrogen bonds · protein-protein
C–L · 1522 Å² buried · 23 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 cofactor, 1 covalent (heme attachment, covalent ligand).

Compared structures

7C9R · Structure of photosynthetic LH1-rc super-complex of thiorhodovibrio strain 970 · the same entry in another collection · chain 1 against 1, 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 H8Z3S2
Every structure of UniProt G1BIY6
Every structure of UniProt G1BIY7
Every structure of UniProt H8Z0X5
Every structure of UniProt G1BIY5
Every structure of UniProt G1BIY9
Every structure of UniProt G1BIY4
Every structure of UniProt H8Z3S4
Every structure of UniProt H8Z3R9
Every structure of UniProt G1BIZ0
Elsewhere: RCSB PDB 7C9R · PDBe 7C9R · UniProt H8Z3S2 · UniProt G1BIY6 · UniProt G1BIY7 · UniProt H8Z0X5 · UniProt G1BIY5 · UniProt G1BIY9 · UniProt G1BIY4 · UniProt H8Z3S4 · UniProt H8Z3R9 · UniProt G1BIZ0

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