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Crystal structure of plant photosystem I-lhci super-complex at 2.8 ångström resolution

Analyse Crystal structure of plant photosystem I-lhci super-complex at 2.8 ångström… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4XK8
Type: protein
Length: 6,350 residues
Chains: 32
Method: x-ray diffraction
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: P10793, I1NGD2, P17227, A4GGC6, E1C9L3, E1C9L1, Q41038, Q32904
Ligands: CLA, BCR, CHL, LHG, LUT, XAT, SF4, LMG, PQN, DGD
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 22 distinct chains · 54% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, a	Photosystem I P700 chlorophyll a apoprotein A1	protein	742	61% helix, 5% strand	—
B, b	Photosystem I P700 chlorophyll a apoprotein A2	protein	733	62% helix, 2% strand	—
C, c	Photosystem I iron-sulfur center (EC 1.97.1.12)	protein	80	14% helix, 21% strand	P10793
D	Uncharacterized protein	protein	141	18% helix, 27% strand	I1NGD2
E	Putative uncharacterized protein	protein	63	5% helix, 35% strand	—
F, f	Photosystem I reaction center subunit III, chloroplastic	protein	151	67% helix, 5% strand	—
G, g	Photosystem I reaction center subunit V, chloroplastic	protein	95	62% helix, 4% strand	—
H, h	Putative uncharacterized protein	protein	90	48% helix, 0% strand	—
I	Photosystem I reaction center subunit VIII	protein	29	86% helix, 0% strand	P17227
J, j	Photosystem I reaction center subunit IX	protein	39	74% helix, 3% strand	A4GGC6
K	Photosystem I reaction center subunit X psak	protein	45	80% helix, 0% strand	E1C9L3
L	Putative uncharacterized protein	protein	153	59% helix, 5% strand	E1C9L1
1, 6	Chlorophyll a-B binding protein 6, chloroplastic	protein	195	52% helix, 2% strand	—
2, 7	Type II chlorophyll A/B binding protein from photosystem I	protein	206	52% helix, 1% strand	Q41038
3	Chlorophyll a-B binding protein 3, chloroplastic	protein	218	51% helix, 1% strand	Q32904
4, 9	Chlorophyll a-B binding protein P4, chloroplastic	protein	196	54% helix, 2% strand	—
d	Uncharacterized protein	protein	140	19% helix, 27% strand	I1NGD2
e	Putative uncharacterized protein	protein	63	5% helix, 37% strand	—
i	Photosystem I reaction center subunit VIII	protein	30	90% helix, 0% strand	P17227
k	Photosystem I reaction center subunit X psak	protein	46	78% helix, 0% strand	E1C9L3
l	Putative uncharacterized protein	protein	151	60% helix, 5% strand	E1C9L1
8	Chlorophyll a-B binding protein 3, chloroplastic	protein	217	53% helix, 2% strand	Q32904

Ligands and binding sites

CLA · Chlorophyll A · ligand · 285 copies · chains A, B, F, J, 3, K, L, H, I, G, 1, 4, 2, a, b, f, j, 8, k, l, h, i, g, 6, 9, 7
BCR · Beta-carotene · ligand · 52 copies · chains A, B, J, F, G, I, K, L, H, 1, 2, 3, 4, a, k, b, f, g, i, j, l, h, 6, 7, 8, 9
CHL · Chlorophyll B · ligand · 24 copies · chains 1, 4, 2, 3, 6, 9, 7, 8
LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 11 copies · chains A, B, 1, 4, 2, 3, a, b, 6, 9, 7, 8
LUT · (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol · ligand · 10 copies · chains 1, F, 4, 2, 3, 6, f, 9, 7, 8
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 · 8 copies · chains 1, 2, 3, 4, 6, 7, 8, f, 9
SF4 · Iron/sulfur cluster · ligand · 6 copies · chains A, B, C, a, b, c
LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 5 copies · chains B, G, 1, 2, 4, b, g, 6, 7, 9
PQN · Phylloquinone · ligand · 4 copies · chains A, J, B, a, j, b
DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 2 copies · chains B, C, b, c
HTG · heptyl 1-thio-beta-D-glucopyranoside · additive · 6 copies · chains A, F, B, J, a, f, b, j
LMT · Dodecyl-beta-D-maltoside · additive · chains B

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	881	0.85	0.86	77	CLA
2	684	0.83	0.86	70	CLA
3	927	0.81	0.83	79	CLA, DGD
4	1155	0.81	0.82	98	CLA, DGD
5	896	0.79	0.81	93	CLA

Interfaces

76 interfaces between chains.

A–B · 3520 Å² buried · 45 hydrogen bonds · protein-protein
a–b · 3491 Å² buried · 42 hydrogen bonds · protein-protein
H–L · 2014 Å² buried · 12 hydrogen bonds · protein-protein
h–l · 2002 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 1631 Å² buried · 24 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

4XK8 · Crystal structure of plant photosystem I-LHCI super-complex at 2.8 angstrom resolution · 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 P10793
Every structure of UniProt I1NGD2
Every structure of UniProt P17227
Every structure of UniProt A4GGC6
Every structure of UniProt E1C9L3
Every structure of UniProt E1C9L1
Every structure of UniProt Q41038
Every structure of UniProt Q32904
Elsewhere: RCSB PDB 4XK8 · PDBe 4XK8 · UniProt P10793 · UniProt I1NGD2 · UniProt P17227 · UniProt A4GGC6 · UniProt E1C9L3 · UniProt E1C9L1 · UniProt Q41038 · UniProt Q32904

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