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Rc-LH1(16) complex from rhodopseudomonas palustris

Analyse Rc-LH1(16) complex from rhodopseudomonas palustris in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6Z5R
Type: protein
Length: 2,336 residues
Chains: 35
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Light-harvesting complex 1 alpha chain; Light-harvesting complex 1 beta chain; H subunit…
UniProt: Q6N9L4, Q6N9L5, A0A4Z9, O83005, A0A4Z7
Ligands: BCL, 6PL, CRT, CDL, U10, BPH, PGT, QAK, FE
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 11 distinct chains · 55% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, E, G, N, R, V, P, A, 1, 3, 5, 7, 9	Light-harvesting complex 1 alpha chain	protein	46	65% helix, 0% strand	Q6N9L4
D, F, B, 8, 0	Light-harvesting complex 1 beta chain	protein	49	65% helix, 4% strand	Q6N9L5
I, K, U, X	Light-harvesting complex 1 beta chain	protein	47	68% helix, 4% strand	Q6N9L5
J	Light-harvesting complex 1 alpha chain	protein	45	64% helix, 0% strand	Q6N9L4
O, S, Q, Z, 2, 4	Light-harvesting complex 1 beta chain	protein	48	67% helix, 4% strand	Q6N9L5
H	H subunit of photosynthetic reaction center complex	protein	247	26% helix, 21% strand	A0A4Z9
L	Reaction center protein L chain	protein	276	62% helix, 4% strand	O83005
M	Reaction center protein M chain	protein	306	61% helix, 3% strand	A0A4Z7
T	Light-harvesting complex 1 alpha chain	protein	48	63% helix, 0% strand	Q6N9L4
Y	Light-harvesting complex 1 alpha chain	protein	45	56% helix, 0% strand	Q6N9L4
6	Light-harvesting complex 1 beta chain	protein	50	64% helix, 4% strand	Q6N9L5

Ligands and binding sites

BCL · Bacteriochlorophyll A · ligand · 36 copies · chains C, D, L, A, B, E, F, G, I, J, K, N, O, P, Q, M, R, S, T, U, V, X, Y, Z, 1, 2, 9, 0, 3, 4, 5, 6, 7, 8
6PL · (4S,7R)-4-hydroxy-N,N,N-trimethyl-9-oxo-7-[(palmitoyloxy)methyl]-3,5,8-trioxa-4-phosphahexacosan-1-aminium 4-oxide · ligand · 24 copies · chains D, C, E, H, L, F, I, K, O, Q, M, G, N, S, U, X, P, Z, B, 2, 4, 3, 5, 6, 8, 0
CRT · Spirilloxanthin · ligand · 16 copies · chains C, D, E, A, F, G, I, J, K, N, O, P, R, S, T, U, V, X, Y, Q, Z, 1, B, 9, 2, 3, 4, 5, 6, 7, 8, 0
CDL · Cardiolipin · ligand · 6 copies · chains E, H, L, M, F, G, J, N, A, 9, 0, P, R, Q
U10 · Ubiquinone-10 · ligand · 5 copies · chains L, A, 7, 9, M, R, T, V
BPH · Bacteriopheophytin A · ligand · 2 copies · chains L, M
PGT · (1S)-2-{[{[(2R)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate · ligand · 2 copies · chains L, 7, 9
QAK · (6~{R},10~{S},14~{R},19~{R},23~{S},24~{E},27~{S}, 28~{E})-2,6,10,14,19,23,27,31-octamethyldotriaconta-24,28-dien-2-ol · ligand · chains M, R, T
FE · Fe (III) ion · metal · chains L, M
LMT · Dodecyl-beta-D-maltoside · additive · 12 copies · chains D, F, G, J, H, K, O, N, M, L, R, P, X, Z, B, 2, 4, 6

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	1113	0.84	0.84	105	QAK, U10
2	969	0.82	0.83	80	empty
3	1159	0.81	0.82	87	BCL
4	1007	0.78	0.79	71	6PL, CRT
5	116	0.78	0.97	28	empty

Interfaces

110 interfaces between chains.

L–M · 4502 Å² buried · 49 hydrogen bonds · protein-protein
H–M · 2938 Å² buried · 36 hydrogen bonds · protein-protein
H–L · 1548 Å² buried · 12 hydrogen bonds · protein-protein
9–0 · 837 Å² buried · 10 hydrogen bonds · protein-protein
P–Q · 831 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 15 modified (formylation).

Compared structures

6Z5R · RC-LH1(16) complex from Rhodopseudomonas palustris · the same entry in another collection · chain C against C, 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 Q6N9L4
Every structure of UniProt Q6N9L5
Every structure of UniProt A0A4Z9
Every structure of UniProt O83005
Every structure of UniProt A0A4Z7
Elsewhere: RCSB PDB 6Z5R · PDBe 6Z5R · UniProt Q6N9L4 · UniProt Q6N9L5 · UniProt A0A4Z9 · UniProt O83005 · UniProt A0A4Z7

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