5VY3 Hydrolase date May 24, 2017
title Thermoplasma Acidophilum 20s Proteasome Using 200kev With St Position
authors M.A.Herzik Jr., M.Wu, G.C.Lander
compound source
Molecule: Proteasome Subunit Alpha
Chain: A, C, E, G, I, K, M, O, Q, S, U, W, Y, 0
Synonym: 20s Proteasome Subunit A, 20s Proteasome Alpha Sub Proteasome Core Protein Psma;
Ec: 3.4.25.1
Engineered: Yes
Organism_scientific: Thermoplasma Acidophilum
Organism_taxid: 2303
Atcc: 25905
Gene: Psma, Ta1288
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Proteasome Subunit Beta
Chain: B, D, F, H, J, L, N, P, R, T, V, X, Z, 1
Synonym: 20s Proteasome Subunit B, 20s Proteasome Beta Subu Proteasome Core Protein Psmb;
Ec: 3.4.25.1
Engineered: Yes

Organism_scientific: Thermoplasma Acidophilum
Organism_taxid: 2303
Atcc: 25905
Gene: Psmb, Ta0612
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 3.10 Å
ligand
enzyme Hydrolase E.C.3.4.25.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, T, N, V, Z, 1, L, J, X, P, B, H, D, R


S, K, Y, E, Q, M, 0, C, A, O, W, I, G, U


Primary referenceAchieving better-than-3-A resolution by single-particle cryo-EM at 200 keV., Herzik MA Jr, Wu M, Lander GC, Nat Methods. 2017 Oct 9. doi: 10.1038/nmeth.4461. PMID:28991891
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (8175 Kb) [Save to disk]
  • Biological Unit Coordinates (5vy3.pdb1.gz) 826 Kb
  • CSU: Contacts of Structural Units for 5VY3
  • Retrieve 5VY3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VY3 from S2C, [Save to disk]
  • View 5VY3 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 5VY3
  • 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 5vy3 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5vy3_W] [5vy3_Z] [5vy3_C] [5vy3_1] [5vy3_A] [5vy3_K] [5vy3_U] [5vy3_X] [5vy3_B] [5vy3_S] [5vy3_T] [5vy3_O] [5vy3_R] [5vy3_Y] [5vy3_H] [5vy3_G] [5vy3_D] [5vy3_E] [5vy3_0] [5vy3_N] [5vy3_V] [5vy3_Q] [5vy3_F] [5vy3_J] [5vy3_P] [5vy3_M] [5vy3_I] [5vy3_L]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5VY3
  • Community annotation for 5VY3 at PDBWiki (http://pdbwiki.org)

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science