5VY4 Hydrolase date May 24, 2017
title Thermoplasma Acidophilum 20s Proteasome Using 200kev With Im
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;
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;
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
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 3.30 Å
enzyme Hydrolase E.C. BRENDA
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] (8045 Kb) [Save to disk]
  • Biological Unit Coordinates (5vy4.pdb1.gz) 812 Kb
  • CSU: Contacts of Structural Units for 5VY4
  • Retrieve 5VY4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VY4 from S2C, [Save to disk]
  • View 5VY4 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 5VY4
  • 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: [5vy4_Q] [5vy4_A] [5vy4_S] [5vy4_T] [5vy4_P] [5vy4_X] [5vy4_D] [5vy4_L] [5vy4_N] [5vy4_E] [5vy4_C] [5vy4_B] [5vy4_U] [5vy4_W] [5vy4_J] [5vy4_K] [5vy4_H] [5vy4_V] [5vy4_Z] [5vy4_O] [5vy4_F] [5vy4_I] [5vy4_Y] [5vy4_0] [5vy4_1] [5vy4_G] [5vy4_R] [5vy4_M]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5VY4
  • Community annotation for 5VY4 at PDBWiki (http://pdbwiki.org)

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