GL1X · GenesisL1 explorer

MolNFT v1 · #172356 · protein

Structure of high-light grown chlorella ohadii photosystem I

6ZZY: “Structure of high-light grown chlorella ohadii photosystem I”. Electron microscopy, 28 ligands (CLA, BCR, LHG). MolNFT v1 #172356 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
6ZZY
Type
protein
Length
4,595 residues
Chains
23
Method
electron microscopy
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
UniProt
W8SY74, W8SUA3, W8SKM2, A0A2P6TKF8, A0A2P6U4S6, A0A2P6TPV8, A0A2P6TZI8, W8SUD1, A0A2P6U0J1, W8SU98, W8SIP9, A0A2P6TPU7, A0A2P6TC44, A0A2P6TT36, A0A2P6TMT4, A0A2P6TQ14, A0A2P6U4K1, A0A2P6TPR7, A0A2P6TS63, A0A2P6TZ50, A0A2P6TMX4, A0A2P6TMI2
Ligands
CLA, BCR, LHG, CHL, LUT, PTY, SF4, DGD, LAP, SQD, 4RF, PQN, PCW, LPX, OLA, QTB…

Structure

electron microscopy · 22 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
A—protein741—W8SY74
B—protein731—W8SUA3
C—protein80—W8SKM2
D—protein143—A0A2P6TKF8
E—protein64—A0A2P6U4S6
F—protein165—A0A2P6TPV8
G—protein99—A0A2P6TZI8
J—protein41—W8SUD1
K—protein86—A0A2P6U0J1
M—protein31—W8SU98
I—protein35—W8SIP9
H—protein94—A0A2P6TPU7
L—protein157—A0A2P6TC44
1, a—protein192—A0A2P6TT36
3—protein241—A0A2P6TMT4
4—protein207—A0A2P6TQ14
5—protein227—A0A2P6U4K1
6—protein231—A0A2P6TPR7
7—protein221—A0A2P6TS63
8—protein220—A0A2P6TZ50
2—protein215—A0A2P6TMX4
9—protein182—A0A2P6TMI2

Ligands and binding sites

  • CLA · Chlorophyll A · ligand · 227 copies · chains A, B, F, J, 3, K, L, H, M, I, 2, G, 9, 1, 7, 8, a, 4, 5, 6
  • BCR · Beta-carotene · ligand · 32 copies · chains A, B, G, 9, F, J, K, I, H, L, 3, 5, 4, 6, 7, 8
  • LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 24 copies · chains A, 3, B, 1, F, 7, 8, J, a, 4, 6, 5, 2, 9, M
  • CHL · Chlorophyll B · ligand · 24 copies · chains 1, 8, a, 4, 3, 6, 5, 7, F, B, 9
  • LUT · (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol · ligand · 22 copies · chains 1, G, a, 3, 4, 5, 6, 7, 8, 2, 9
  • PTY · Phosphatidylethanolamine · ligand · 6 copies · chains B, F, J, A, 3, 5, 7, 4, 1, 8, 9
  • SF4 · Iron/sulfur cluster · ligand · 3 copies · chains A, B, C
  • DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 3 copies · chains A, J, B, C, 4, 8
  • LAP · [2-((1-oxododecanoxy-(2-hydroxy-3-propanyl))-phosphonate-oxy)-ethyl]-trimethylammonium · ligand · 3 copies · chains F, 1, A, K, 3
  • SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · 3 copies · chains B, G, 9, H, L, 2, 6, 7
  • 4RF · Tripalmitoylglycerol · ligand · 3 copies · chains J, 7, 8, F
  • PQN · Phylloquinone · ligand · 2 copies · chains A, B
  • PCW · 1,2-dioleoyl-sn-glycero-3-phosphocholine · ligand · 2 copies · chains F, 6, 7
  • LPX · (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate · ligand · 2 copies · chains F, J, a
  • OLA · Oleic acid · ligand · 2 copies · chains 1, 8
  • QTB · (3~{E},5~{E},7~{E})-6-methyl-8-[(6~{R})-2,2,6-trimethylcyclohexyl]octa-3,5,7-trien-2-one · ligand · 2 copies · chains a, 3
  • PLM · Palmitic acid · ligand · 2 copies · chains a, 8, 6, 7
  • DGA · Diacyl glycerol · ligand · 2 copies · chains 5, F, 8
  • CL0 · Chlorophyll A isomer · ligand · chains A, B
  • 3PH · 1,2-diacyl-glycerol-3-sn-phosphate · ligand · chains A, J, 7
  • ERG · Ergosterol · ligand · chains G, 1
  • RRX · (3R)-beta,beta-caroten-3-ol · ligand · chains A, J
  • ECH · beta,beta-caroten-4-one · ligand · chains B, M
  • GG0 · 2-(2-azanylethanoylamino)ethanoic acid · ligand · chains a
  • SPH · Sphingosine · ligand · chains 5, 6
  • 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 · chains 7
  • C7Z · (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E}, 9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol · ligand · chains 7, 8
  • A8S · (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid · ligand · chains 9
  • LMT · Dodecyl-beta-D-maltoside · additive · 4 copies · chains A, 3, 7, G, 1, M, I, 2

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Compared structures

  • 6ZZY · Structure of high-light grown Chlorella ohadii photosystem I · the same entry in another collection · chain 9 against 9, TM-score 1.00

Analyse

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