OCA Atlas for 5D6Y

5D6Y

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

M3L

enzyme

Primary reference

Reader domain specificity and lysine demethylase-4 family function., Su Z, Wang F, Lee JH, Stephens KE, Papazyan R, Voronina E, Krautkramer KA, Raman A, Thorpe JJ, Boersma MD, Kuznetsov VI, Miller MD, Taverna SD, Phillips GN Jr, Denu JM, Nat Commun. 2016 Nov 14;7:13387. doi: 10.1038/ncomms13387. PMID:27841353

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (238 Kb) [Save to disk]

Biological Unit Coordinates (5d6y.pdb1.gz) 41 Kb

Biological Unit Coordinates (5d6y.pdb2.gz) 41 Kb

Biological Unit Coordinates (5d6y.pdb3.gz) 39 Kb

Biological Unit Coordinates (5d6y.pdb4.gz) 39 Kb

Biological Unit Coordinates (5d6y.pdb5.gz) 38 Kb

Biological Unit Coordinates (5d6y.pdb6.gz) 39 Kb

LPC: Ligand-Protein Contacts for 5D6Y

CSU: Contacts of Structural Units for 5D6Y

Structure Factors (505 Kb)

Retrieve 5D6Y in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 5D6Y from S2C, [Save to disk]

Re-refined 5d6y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5D6Y 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: [5d6y] [5d6y_A] [5d6y_B] [5d6y_C] [5d6y_D] [5d6y_E] [5d6y_F] [5d6y_a] [5d6y_b] [5d6y_c] [5d6y_d]

SWISS-PROT database:

Domain found in 5D6Y: [TUDOR ] by SMART

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