OCA Atlas for 3DFY

3DFY

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

enzyme

Gene

Gene
Ontology

Chain	Function	Process	Component
M, A, O, L, I, D, P, H, B, F, J, K, N, E, G, C

Primary reference

Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening., Kalyanaraman C, Imker HJ, Fedorov AA, Fedorov EV, Glasner ME, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP, Structure. 2008 Nov;16(11):1668-77. PMID:19000819

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (847 Kb) [Save to disk]

Biological Unit Coordinates (3dfy.pdb1.gz) 424 Kb

Biological Unit Coordinates (3dfy.pdb2.gz) 426 Kb

LPC: Ligand-Protein Contacts for 3DFY

CSU: Contacts of Structural Units for 3DFY

Likely Quarternary Molecular Structure file(s) for 3DFY

Structure Factors (4197 Kb)

Retrieve 3DFY in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 3DFY from S2C, [Save to disk]

Re-refined 3dfy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3DFY 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: [3dfy_M] [3dfy_N] [3dfy_O] [3dfy_P] [3dfy] [3dfy_A] [3dfy_B] [3dfy_C] [3dfy_D] [3dfy_E] [3dfy_F] [3dfy_G] [3dfy_H] [3dfy_I] [3dfy_J] [3dfy_K] [3dfy_L]

SWISS-PROT database: [Q9WXM1]

Domain found in 3DFY: [MR_MLE ] by SMART

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