OCA Atlas for 2VKM

2VKM

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

BSD BindingDB

enzyme

Gene
Ontology

Chain	Function	Process	Component
A, B, C, D

Primary reference

Potent memapsin 2 (beta-secretase) inhibitors: design, synthesis, protein-ligand X-ray structure, and in vivo evaluation., Ghosh AK, Kumaragurubaran N, Hong L, Kulkarni S, Xu X, Miller HB, Reddy DS, Weerasena V, Turner R, Chang W, Koelsch G, Tang J, Bioorg Med Chem Lett. 2008 Feb 1;18(3):1031-6. Epub 2008 Jan 3. PMID:18180160

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (267 Kb) [Save to disk]

Biological Unit Coordinates (2vkm.pdb1.gz) 68 Kb

Biological Unit Coordinates (2vkm.pdb2.gz) 69 Kb

Biological Unit Coordinates (2vkm.pdb3.gz) 70 Kb

Biological Unit Coordinates (2vkm.pdb4.gz) 68 Kb

LPC: Ligand-Protein Contacts for 2VKM

CSU: Contacts of Structural Units for 2VKM

Likely Quarternary Molecular Structure file(s) for 2VKM

Structure Factors (1684 Kb)

Retrieve 2VKM in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 2VKM from S2C, [Save to disk]

Re-refined 2vkm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2VKM 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: [2vkm] [2vkm_A] [2vkm_B] [2vkm_C] [2vkm_D]

SWISS-PROT database: [P56817]

Belongs to the β-amyloid cleaving enzyme (bace1) family

according to TCDB.

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