5YMS	Viral Protein	date	Oct 22, 2017
title	Structural Basis Of Glycan Specificity And Identification Of Glycan Binding Cavity In Human P[19] Rotavirus
authors	X.Sun, L.Dandi, Z.Duan
compound		source
Molecule: Outer Capsid Protein Vp4 Chain: A, B, C, D, E, F, G, H Synonym: Rotavirus Vp8 Protein Engineered: Yes Other_details: P[19] Vp8 And Lnt		Organism_scientific: Human Rotavirus A Organism_taxid: 10941 Expression_system: Escherichia Coli-Pichia Pastoris Shuttle Ppparg4; Expression_system_taxid: 1182032
symmetry	Space Group: C 1 2 1	R_factor 0.181 R_Free 0.213
crystal cell	length a length b length c angle alpha angle beta angle gamma 179.776 129.346 86.365 90.00 116.07 90.00
method	X-Ray Diffraction	resolution	2.10 Å
ligand	A2G, GAL, NAG	enzyme
Gene Ontology	Chain Function Process Component F, A, E, B, H, C, D, G
Primary reference	Glycan Binding Specificity and Mechanism of Human and Porcine P[6]/P[19] Rotavirus VP8*s., Sun X, Li D, Qi J, Chai W, Wang L, Wang L, Peng R, Wang H, Zhang Q, Pang L, Kong X, Wang H, Jin M, Gao GF, Duan Z, J Virol. 2018 May 2. pii: JVI.00538-18. doi: 10.1128/JVI.00538-18. PMID:29720519

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (444 Kb) [Save to disk] Biological Unit Coordinates (5yms.pdb1.gz) 59 Kb Biological Unit Coordinates (5yms.pdb2.gz) 58 Kb Biological Unit Coordinates (5yms.pdb3.gz) 58 Kb Biological Unit Coordinates (5yms.pdb4.gz) 58 Kb Biological Unit Coordinates (5yms.pdb5.gz) 58 Kb Biological Unit Coordinates (5yms.pdb6.gz) 59 Kb Biological Unit Coordinates (5yms.pdb7.gz) 58 Kb Biological Unit Coordinates (5yms.pdb8.gz) 59 Kb LPC: Ligand-Protein Contacts for 5YMS CSU: Contacts of Structural Units for 5YMS Structure Factors (1551 Kb) Retrieve 5YMS in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5YMS from S2C, [Save to disk]

View 5YMS 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 5YMS

Ramachandran plot from PDBSum

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: [5yms_B] [5yms_F] [5yms_A] [5yms_G] [5yms_E] [5yms_D] [5yms_H] [5yms_C] SWISS-PROT database: Domain organization of by SWISSPFAM

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