OCA Atlas for 5VYP

5VYP

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

GOL, PIO, SO4

enzyme

Gene
Ontology

Chain	Function	Process	Component
X, D, E, U, T, K, G, V, I, Q, H, A, W, F, P, R, N, B, O, C, M, S, J, L

Primary reference

Structure of the defensin NsD7 in complex with PIP2 reveals that defensin:lipid oligomer topologies are dependent on lipid type., Jarva M, Lay FT, Hulett MD, Kvansakul M, FEBS Lett. 2017 Jul 25. doi: 10.1002/1873-3468.12761. PMID:28741756

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (220 Kb) [Save to disk]

Biological Unit Coordinates (5vyp.pdb1.gz) 206 Kb

LPC: Ligand-Protein Contacts for 5VYP

CSU: Contacts of Structural Units for 5VYP

Structure Factors (1614 Kb)

Retrieve 5VYP in mmCIF format [Save to disk]

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

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

View 5VYP 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: [5vyp_A] [5vyp_B] [5vyp_C] [5vyp_D] [5vyp_E] [5vyp_F] [5vyp_G] [5vyp_H] [5vyp_I] [5vyp_J] [5vyp_K] [5vyp_L] [5vyp_M] [5vyp_N] [5vyp_O] [5vyp_P] [5vyp_Q] [5vyp_R] [5vyp_S] [5vyp_T] [5vyp_U] [5vyp_V] [5vyp_W] [5vyp_X]

SWISS-PROT database:

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