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MolNFT v1 · #186407 · protein

High-resolution structure of photosystem II from the mesophilic cyanobacterium, synechocystis sp. pcc 6803

7RCV: “High-resolution structure of photosystem II from the mesophilic cyanobacterium, synechocystis sp. pcc 6803”. Electron microscopy, 15 ligands (CLA, BCR, SQD). MolNFT v1 #186407 on GenesisL1: 3D structure, binding sites and pockets in…

PDB
7RCV
Type
protein
Length
5,544 residues
Chains
42
Method
electron microscopy
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
UniProt
P16033, P05429, P09193, P09192, P09190, P09191, P14835, Q54697, P73070, P15819, Q55354, P72701, P10549, P73048, P73676, P74787, Q55332, Q55013, P72575, Q55438, P73528
Ligands
CLA, BCR, SQD, LHG, LMG, DGD, PHO, PL9, HEM, OEX, BCT, RRX, CA, FE2, CL

Structure

electron microscopy · 21 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
A, a—protein334—P16033
B, b—protein503—P05429
C, c—protein450—P09193
D, d—protein341—P09192
E, e—protein78—P09190
F, f—protein35—P09191
H, h—protein63—P14835
I, i—protein36—Q54697
J, j—protein39—P73070
K, k—protein37—P15819
L, l—protein39—Q55354
M, m—protein31—P72701
O, o—protein243—P10549
Q, q—protein119—P73048
R, r—protein34—P73676
T, t—protein30—P74787
U, u—protein95—Q55332
V, v—protein135—Q55013
X, x—protein38—P72575
Y, y—protein32—Q55438
Z, z—protein60—P73528

Ligands and binding sites

  • CLA · Chlorophyll A · ligand · 70 copies · chains A, D, I, B, H, L, M, t, C, K, Y, Z, T, X, a, d, i, b, h, l, m, c, k, y, z, x
  • BCR · Beta-carotene · ligand · 18 copies · chains A, I, B, M, t, C, K, Z, D, F, J, Y, a, i, T, b, m, c, k, z, d, f, j, y
  • SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · 14 copies · chains A, C, D, K, T, b, h, l, B, L, m, t, F, R, X, H, M, a, c, d, k, f, r, x
  • LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 14 copies · chains A, C, D, B, L, M, T, E, F, Z, a, c, d, b, l, m, t, e, f, z
  • LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 12 copies · chains A, C, I, b, B, L, M, J, K, Y, D, F, a, c, i, l, m, j, k, y, d, f
  • DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 8 copies · chains A, C, J, D, V, B, H, a, c, j, d, v, b, h
  • PHO · Pheophytin A · ligand · 4 copies · chains A, D, a, d
  • PL9 · 2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2, 6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone · ligand · 4 copies · chains A, D, F, X, L, T, a, d, f, x, l, t
  • HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains E, F, R, V, e, f, r, v
  • OEX · Ca-MN4-O5 cluster · ligand · 2 copies · chains A, C, a, c
  • BCT · Bicarbonate ion · ligand · 2 copies · chains A, D, a, d
  • RRX · (3R)-beta,beta-caroten-3-ol · ligand · 2 copies · chains H, X, h, x
  • CA · Calcium ion · metal · 6 copies · chains K, Y, B, U, C, V, k, y, b, u, c, v
  • FE2 · Fe (II) ion · metal · 2 copies · chains A, D, a, d
  • CL · Chloride ion · ion · 4 copies · chains A, D, C, a, d, c
  • LMT · Dodecyl-beta-D-maltoside · additive · 62 copies · chains A, b, C, I, B, D, H, Z, E, F, R, J, K, M, t, L, l, T, X, Y, a, c, i, d, h, z, e, f, r, j, k, m, x, y

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

Compared structures

  • 7RCV · High-resolution structure of photosystem II from the mesophilic cyanobacterium… · the same entry in another collection · chain L against L, TM-score 1.00

Analyse

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