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State transition supercomplex psi-lhci-lhcii from the LHCBM1 lacking mutant of chlamydomonas reinhardtii

Analyse State transition supercomplex psi-lhci-lhcii from the LHCBM1 lacking mutant of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7DZ8
Type: protein
Length: 5,986 residues
Chains: 29
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Photosystem I P700 chlorophyll a apoprotein A1; Photosystem I P700 chlorophyll a…
EC: 1.97.1.12
UniProt: P12154, P09144, Q00914, Q39615, P12352, P12356, P14224, P13352, A8IFG7, P59777, P14225, A8IL32, A8JCL6, Q05093, A8IKC8, A8JF10, Q75VZ0, Q75VY8, Q75VY6, Q84Y02, Q75VY7, A8ITV3, Q93WE0, Q93WL4, Q9ZSJ4
Ligands: CLA, BCR, CHL, LHG, LUT, XAT, LMG, NEX, LMU, SF4, PQN, DGD
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 28 distinct chains · 51% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Photosystem I P700 chlorophyll a apoprotein A1 (EC 1.97.1.12)	protein	741	61% helix, 5% strand	P12154
B	Photosystem I P700 chlorophyll a apoprotein A2 (EC 1.97.1.12)	protein	733	59% helix, 3% strand	P09144
C	Photosystem I iron-sulfur center (EC 1.97.1.12)	protein	80	16% helix, 15% strand	Q00914
D	Photosystem I reaction center subunit II, chloroplastic	protein	143	13% helix, 22% strand	Q39615
E	Photosystem I reaction center subunit IV, chloroplastic	protein	63	0% helix, 37% strand	P12352
F	Photosystem I reaction center subunit III, chloroplastic	protein	165	56% helix, 5% strand	P12356
G	Photosystem I reaction center subunit V, chloroplastic	protein	94	54% helix, 0% strand	P14224
H	Photosystem I reaction center subunit VI, chloroplastic	protein	100	47% helix, 2% strand	P13352
I	Photosystem I reaction center subunit VIII	protein	42	60% helix, 2% strand	A8IFG7
J	Photosystem I reaction center subunit IX	protein	41	68% helix, 2% strand	P59777
K	Photosystem I reaction center subunit psak, chloroplastic	protein	86	49% helix, 8% strand	P14225
L	Psi subunit V	protein	159	60% helix, 4% strand	A8IL32
O	Photosystem I subunit O	protein	97	59% helix, 0% strand	A8JCL6
1, a	Chlorophyll a-B binding protein, chloroplastic	protein	194	48% helix, 2% strand	Q05093
2	Chlorophyll a-B binding protein, chloroplastic	protein	217	57% helix, 0% strand	A8IKC8
3	Chlorophyll a-B binding protein, chloroplastic	protein	220	49% helix, 0% strand	A8JF10
4	Chlorophyll a-B binding protein, chloroplastic	protein	210	52% helix, 1% strand	Q75VZ0
5	Chlorophyll a-B binding protein, chloroplastic	protein	227	45% helix, 3% strand	Q75VY8
6	Chlorophyll a-B binding protein, chloroplastic	protein	230	44% helix, 5% strand	Q75VY6
7	Chlorophyll a-B binding protein, chloroplastic	protein	213	53% helix, 1% strand	Q84Y02
8	Chlorophyll a-B binding protein, chloroplastic	protein	216	53% helix, 0% strand	Q75VY7
9	Chlorophyll a-B binding protein, chloroplastic	protein	183	49% helix, 0% strand	A8ITV3
X	Chlorophyll a-B binding protein, chloroplastic	protein	221	49% helix, 0% strand	Q93WE0
Y	Chlorophyll a-B binding protein, chloroplastic	protein	219	45% helix, 2% strand	Q93WL4
Z	Chlorophyll a-B binding protein, chloroplastic	protein	221	48% helix, 2% strand	Q93WL4
U	Chlorophyll a-B binding protein, chloroplastic	protein	219	49% helix, 1% strand	Q93WL4
V	Chlorophyll a-B binding protein, chloroplastic	protein	238	48% helix, 2% strand	Q9ZSJ4
W	Chlorophyll a-B binding protein, chloroplastic	protein	220	49% helix, 1% strand	Q93WE0

Ligands and binding sites

CLA · Chlorophyll A · ligand · 298 copies · chains A, B, F, J, 3, K, O, L, H, I, G, 9, 1, 2, V, 8, a, 4, 7, 5, 6, X, Y, Z, U, W
BCR · Beta-carotene · ligand · 40 copies · chains A, O, B, J, F, G, 9, I, 2, K, L, H, 1, a, 3, 5, 4, 6, 7, 8
CHL · Chlorophyll B · ligand · 36 copies · chains X, Z, Y, U, W, V
LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 27 copies · chains A, B, I, 2, 9, 1, H, L, O, Z, 8, a, 4, 3, 5, 7, 6, X, Y, U, V, W
LUT · (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol · ligand · 22 copies · chains 1, a, 2, 3, 4, 5, 6, 7, 8, 9, X, Y, Z, U, V, W
XAT · (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-tetrahydro-beta,beta-carotene-3,3'-diol · ligand · 16 copies · chains 1, a, 2, 3, 4, 5, 6, 7, 8, 9, X, Y, O, Z, U, V, W
LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 11 copies · chains A, J, 7, H, L, 2, B, F, 4, 6, 8, 1, 9, V
NEX · (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R, 6R)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13, 15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol · ligand · 8 copies · chains 5, 6, 4, X, Y, Z, U, V, W
LMU · Dodecyl-alpha-D-maltoside · ligand · 7 copies · chains A, 3, K, G, 1, 5, 6, 4, 8
SF4 · Iron/sulfur cluster · ligand · 3 copies · chains A, B, C
PQN · Phylloquinone · ligand · 2 copies · chains A, J, B
DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · chains B, C, D

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	1145	0.86	0.86	106	CLA
2	1026	0.81	0.82	94	CLA, DGD
3	604	0.80	0.85	61	empty
4	1078	0.74	0.77	122	CLA, LHG
5	1045	0.73	0.76	91	CLA, LHG, LMG

Interfaces

66 interfaces between chains.

A–B · 3541 Å² buried · 47 hydrogen bonds · protein-protein
H–L · 2101 Å² buried · 29 hydrogen bonds · protein-protein
C–D · 1690 Å² buried · 30 hydrogen bonds · protein-protein
B–G · 1287 Å² buried · 17 hydrogen bonds · protein-protein
B–H · 1192 Å² buried · 25 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide, 1 modified (disulfide, phosphorylation).

Compared structures

7DZ8 · State transition supercomplex PSI-LHCI-LHCII from the LhcbM1 lacking mutant of… · the same entry in another collection · chain K against K, 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 P12154
Every structure of UniProt P09144
Every structure of UniProt Q00914
Every structure of UniProt Q39615
Every structure of UniProt P12352
Every structure of UniProt P12356
Every structure of UniProt P14224
Every structure of UniProt P13352
Every structure of UniProt A8IFG7
Every structure of UniProt P59777
Every structure of UniProt P14225
Every structure of UniProt A8IL32
Every structure of UniProt A8JCL6
Every structure of UniProt Q05093
Every structure of UniProt A8IKC8
Every structure of UniProt A8JF10
Every structure of UniProt Q75VZ0
Every structure of UniProt Q75VY8
Every structure of UniProt Q75VY6
Every structure of UniProt Q84Y02
Every structure of UniProt Q75VY7
Every structure of UniProt A8ITV3
Every structure of UniProt Q93WE0
Every structure of UniProt Q93WL4
Every structure of UniProt Q9ZSJ4
Elsewhere: RCSB PDB 7DZ8 · PDBe 7DZ8 · UniProt P12154 · UniProt P09144 · UniProt Q00914 · UniProt Q39615 · UniProt P12352 · UniProt P12356 · UniProt P14224 · UniProt P13352 · UniProt A8IFG7 · UniProt P59777 · UniProt P14225 · UniProt A8IL32 · UniProt A8JCL6 · UniProt Q05093 · UniProt A8IKC8 · UniProt A8JF10 · UniProt Q75VZ0 · UniProt Q75VY8 · UniProt Q75VY6 · UniProt Q84Y02 · UniProt Q75VY7 · UniProt A8ITV3 · UniProt Q93WE0 · UniProt Q93WL4 · UniProt Q9ZSJ4

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