OCA Atlas for 4DPG

4DPG

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

ALA, APC, LYS, MG

enzyme

Gene
Ontology

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

Primary reference

Structural Switch of Lysyl-tRNA Synthetase between Translation and Transcription., Ofir-Birin Y, Fang P, Bennett SP, Zhang HM, Wang J, Rachmin I, Shapiro R, Song J, Dagan A, Pozo J, Kim S, Marshall AG, Schimmel P, Yang XL, Nechushtan H, Razin E, Guo M, Mol Cell. 2013 Jan 10;49(1):30-42. doi: 10.1016/j.molcel.2012.10.010. Epub 2012, Nov 15. PMID:23159739

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1350 Kb) [Save to disk]

Biological Unit Coordinates (4dpg.pdb1.gz) 340 Kb

Biological Unit Coordinates (4dpg.pdb2.gz) 341 Kb

Biological Unit Coordinates (4dpg.pdb3.gz) 343 Kb

Biological Unit Coordinates (4dpg.pdb4.gz) 342 Kb

LPC: Ligand-Protein Contacts for 4DPG

CSU: Contacts of Structural Units for 4DPG

Structure Factors (992 Kb)

Retrieve 4DPG in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 4DPG from S2C, [Save to disk]

Re-refined 4dpg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 4DPG 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: [4dpg] [4dpg_A] [4dpg_B] [4dpg_C] [4dpg_D] [4dpg_E] [4dpg_F] [4dpg_G] [4dpg_H] [4dpg_I] [4dpg_J] [4dpg_K] [4dpg_L]

SWISS-PROT database:

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