OCA Atlas for 5VN8

5VN8

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

BMA, MAN, NAG

enzyme

Gene
Ontology

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

Primary reference

Open and closed structures reveal allostery and pliability in the HIV-1 envelope spike., Ozorowski G, Pallesen J, de Val N, Lyumkis D, Cottrell CA, Torres JL, Copps J, Stanfield RL, Cupo A, Pugach P, Moore JP, Wilson IA, Ward AB, Nature. 2017 Jul 20;547(7663):360-363. doi: 10.1038/nature23010. Epub 2017 Jul, 12. PMID:28700571

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (388 Kb) [Save to disk]

Biological Unit Coordinates (5vn8.pdb1.gz) 368 Kb

LPC: Ligand-Protein Contacts for 5VN8

CSU: Contacts of Structural Units for 5VN8

Retrieve 5VN8 in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 5VN8 from S2C, [Save to disk]

View 5VN8 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.

Visual 3D analysis of 5VN8

Cartoon representation from PDB Cartoon

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

Crystal Contacts, from CryCo at Weizmann Institute

Fold representative 5vn8 from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5vn8_D] [5vn8_E] [5vn8_F] [5vn8_G] [5vn8_H] [5vn8_I] [5vn8_J] [5vn8_K] [5vn8_L] [5vn8_A] [5vn8_B] [5vn8_C]

SWISS-PROT database:

Domain organization of by SWISSPFAM

Other resources with information on 5VN8

Community annotation for 5VN8 at PDBWiki (http://pdbwiki.org)

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