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

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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