GL1X · GenesisL1 explorer

MolNFT v1 · #136736 · protein

Re-refinement of crystal structure of photosystem II complex

5V2C: “Re-refinement of crystal structure of photosystem II complex”. X-ray diffraction, 16 ligands (CLA, BCR, LMG). MolNFT v1 #136736 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
5V2C
Type
protein
Length
5,280 residues
Chains
38
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
UniProt
P51765, D0VWR1, D0VWR7, D0VWR8, P12238, P12239, P19052, P12240, Q7DGD4, P19054, P12241, P12312, D0VWR2, P12313, P56152, P0A387, D0VWR3, D0VWR4, D0VWR5
Ligands
CLA, BCR, LMG, LHG, SQD, DGD, PHO, PL9, BCT, OEX, HEM, HEC, CA, MG, FE2, CL

Structure

x-ray diffraction · 23 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
A, a—protein334—P51765
B—protein504—D0VWR1
C—protein451—D0VWR7
D, d—protein342—D0VWR8
E, e—protein81—P12238
F—protein34—P12239
H, h—protein65—P19052
I, i—protein38—P12240
J, j—protein39—Q7DGD4
K, k—protein37—P19054
L, l—protein37—P12241
M—protein34—P12312
O, o—protein245—D0VWR2
T, t—protein30—P12313
U, u—protein97—P56152
V, v—protein137—P0A387
Y, y—protein29—D0VWR3
X, x—protein40—D0VWR4
Z, z—protein62—D0VWR5
b—protein506—D0VWR1
c—protein458—D0VWR7
f—protein32—P12239
m—protein35—P12312

Ligands and binding sites

  • CLA · Chlorophyll A · ligand · 70 copies · chains A, D, T, I, B, H, L, M, C, K, Y, Z, X, a, d, t, i, b, h, l, m, c, k, y, z, x
  • BCR · Beta-carotene · ligand · 22 copies · chains A, I, B, M, t, C, K, Z, D, F, J, H, X, Y, T, b, a, i, m, c, k, z, d, f, j, h, x, y
  • LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 14 copies · chains A, C, I, B, D, L, M, H, X, J, K, Y, Z, F, a, c, i, b, d, l, m, j, k, y, z, h, x, f
  • LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 12 copies · chains A, C, K, B, D, L, M, T, E, F, a, c, k, b, d, l, m, t, e, f
  • SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · 11 copies · chains A, C, D, J, K, T, b, E, F, X, a, c, d, k, B, t, L, M, l, h, m, f, x
  • DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 10 copies · chains A, C, J, D, V, E, F, B, H, a, c, j, d, v, e, f, 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
  • BCT · Bicarbonate ion · ligand · 3 copies · chains A, D, a, d, M, m
  • OEX · Ca-MN4-O5 cluster · ligand · 2 copies · chains A, C, a, c
  • HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains E, F, e, f
  • HEC · Heme C · ligand · 2 copies · chains V, v
  • CA · Calcium ion · metal · 6 copies · chains B, O, b, c, h, o
  • MG · Magnesium ion · metal · 4 copies · chains F, J, f, v, j
  • FE2 · Fe (II) ion · metal · 2 copies · chains A, D, a, d
  • CL · Chloride ion · ion · 6 copies · chains A, D, C, a, d, c
  • PGE · Triethylene glycol · additive · 65 copies · chains b, J, B, D, V, C, E, H, X, I, O, T, U, Y, Z, a, i, c, t, d, h, x, j, o, u
  • GOL · Glycerol · additive · 60 copies · chains A, O, b, D, E, V, B, U, H, M, t, C, T, X, F, L, a, d, e, v, u, m, c, f, l, o, j, y
  • PG4 · Tetraethylene glycol · additive · 57 copies · chains A, B, H, C, D, X, E, I, J, Y, K, U, V, a, b, h, c, k, d, x, e, j, i, M, l
  • HTG · heptyl 1-thio-beta-D-glucopyranoside · additive · 24 copies · chains B, O, a, C, D, H, A, b, V, c, t, o, d, h
  • EDO · 1,2-ethanediol · additive · 22 copies · chains A, B, L, H, C, D, E, I, J, O, V, X, c, b, d, o, e, i
  • LMT · Dodecyl-beta-D-maltoside · additive · 18 copies · chains A, D, b, B, H, X, C, I, E, F, J, M, l, m, T, Y, a, d, h, x, c, i, e, f, j, y, t, L, u
  • P6G · Hexaethylene glycol · additive · 17 copies · chains A, I, B, C, D, H, X, E, T, b, c, d, x, j
  • 1PE · Pentaethylene glycol · additive · 7 copies · chains B, L, m, V, e, f, j, x
  • 2PE · Nonaethylene glycol · additive · chains V
  • PE8 · 3,6,9,12,15,18,21-heptaoxatricosane-1,23-diol · additive · chains i

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

Compared structures

  • 5V2C · Re-refinement of crystal structure of photosystem II complex · the same entry in another collection · chain L against L, TM-score 1.00

Analyse

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