OCA Atlas for 5DN2

5DN2

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

DIO, GOL

enzyme

Gene
Ontology

Chain	Function	Process	Component
C, B, A, D
G, F, E

Primary reference

Structural studies of neuropilin-2 reveal a zinc ion binding site remote from the vascular endothelial growth factor binding pocket., Tsai YC, Fotinou C, Rana R, Yelland T, Frankel P, Zachary I, Djordjevic S, FEBS J. 2016 May;283(10):1921-34. doi: 10.1111/febs.13711. Epub 2016 Apr 1. PMID:26991001

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (215 Kb) [Save to disk]

Biological Unit Coordinates (5dn2.pdb1.gz) 54 Kb

Biological Unit Coordinates (5dn2.pdb2.gz) 53 Kb

Biological Unit Coordinates (5dn2.pdb3.gz) 54 Kb

Biological Unit Coordinates (5dn2.pdb4.gz) 54 Kb

LPC: Ligand-Protein Contacts for 5DN2

CSU: Contacts of Structural Units for 5DN2

Structure Factors (3134 Kb)

Retrieve 5DN2 in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 5DN2 from S2C, [Save to disk]

Re-refined 5dn2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5DN2 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: [5dn2] [5dn2_A] [5dn2_B] [5dn2_C] [5dn2_D] [5dn2_E] [5dn2_F] [5dn2_G]

SWISS-PROT database:

Domain found in 5DN2: [FA58C ] by SMART

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