OCA Atlas for 5Y5S

5Y5S

date

authors

compound

source

symmetry

R_factor

R_Free

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma

method

X-Ray Diffraction

resolution

ligand

BCL, BPH, CA, CDL, CRT, FE, GOL, HEC, LDA, LHG, LMT, MG, MQ8, PEF, PGV, SO4, UNL, UQ8

enzyme

Gene
Ontology

Chain	Function	Process	Component
C
H	electron transporter, transf...
L
M
T, V, G, Z, 6, 2, N, R, 8, B, P, 0, E, X, 4, J	electron transporter, transf...
U, O, K, S, 7, Q, 1, Y, 3, A, 9, F, D, 5, W, I	electron transporter, transf...

Primary reference

Structure of photosynthetic LH1-RC supercomplex at 1.9 A resolution., Yu LJ, Suga M, Wang-Otomo ZY, Shen JR, Nature. 2018 Apr;556(7700):209-213. doi: 10.1038/s41586-018-0002-9. Epub 2018 Apr, 4. PMID:29618814

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1197 Kb) [Save to disk]

Biological Unit Coordinates (5y5s.pdb1.gz) 1154 Kb

LPC: Ligand-Protein Contacts for 5Y5S

CSU: Contacts of Structural Units for 5Y5S

Structure Factors (7107 Kb)

Retrieve 5Y5S in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 5Y5S from S2C, [Save to disk]

View 5Y5S in 3D

Proteopedia, because life has more than 2D.

On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.

On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5y5s_0] [5y5s_1] [5y5s_2] [5y5s_3] [5y5s_4] [5y5s_5] [5y5s_6] [5y5s_7] [5y5s_8] [5y5s_9] [5y5s_A] [5y5s_B] [5y5s_C] [5y5s_D] [5y5s_E] [5y5s_F] [5y5s_G] [5y5s_H] [5y5s_I] [5y5s_J] [5y5s_K] [5y5s_L] [5y5s_M] [5y5s_N] [5y5s_O] [5y5s_P] [5y5s_Q] [5y5s_R] [5y5s_S] [5y5s_T] [5y5s_U] [5y5s_V] [5y5s_W] [5y5s_X] [5y5s_Y] [5y5s_Z]

SWISS-PROT database:

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