5KHR Cell Cycle date Jun 15, 2016
title Model Of Human Anaphase-Promoting Complexcyclosome Complex Deletion Mutant) In Complex With The E2 Ube2cubch10 Poised Ubiquitin Ligation To Substrate (Apcc-Cdc20-Substrate-Ube2
authors R.Vanderlinden, M.Yamaguchi, P.Dube, D.Haselbach, H.Stark, B.A.Sc
compound source
Molecule: Anaphase-Promoting Complex Subunit 1
Chain: A
Synonym: Apc1,Cyclosome Subunit 1,Mitotic Checkpoint Regula Testis-Specific Gene 24 Protein;
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Anapc1, Tsg24
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Anaphase-Promoting Complex Subunit 11
Chain: B
Synonym: Apc11,Cyclosome Subunit 11,Hepatocellular Carcinom Associated Ring Finger Protein;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Anapc11, Hspc214
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Cell Division Cycle Protein 23 Homolog
Chain: C, P
Synonym: Anaphase-Promoting Complex Subunit 8,Apc8,Cyclosom 8;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cdc23, Anapc8
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Anaphase-Promoting Complex Subunit 16
Chain: E
Synonym: Apc16,Cyclosome Subunit 16
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Anapc16, C10orf104, Cenp-27
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Cell Division Cycle Protein 27 Homolog
Chain: F, H
Synonym: Anaphase-Promoting Complex Subunit 3,Apc3,Cdc27 Ho Cdc27hs,H-Nuc;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cdc27, Anapc3, D0s1430e, D17s978e
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Anaphase-Promoting Complex Subunit Cdc26
Chain: G, W
Synonym: Anaphase-Promoting Complex Subunit 12,Apc12,Cell D Cycle Protein 26 Homolog;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cdc26, Anapc12, C9orf17
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Anaphase-Promoting Complex Subunit 4
Chain: I
Synonym: Apc4,Cyclosome Subunit 4
Engineered: Yes
Other_details: Contains The Remnant Of A C-Terminal Linker 3c Protease Site.;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Anapc4, Apc4
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Cell Division Cycle Protein 16 Homolog
Chain: J, K
Synonym: Anaphase-Promoting Complex Subunit 6,Apc6,Cdc16 Ho Cdc16hs,Cyclosome Subunit 6;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cdc16, Anapc6
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Anaphase-Promoting Complex Subunit 10
Chain: L
Synonym: Apc10,Cyclosome Subunit 10
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Anapc10, Apc10
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Anaphase-Promoting Complex Subunit 13
Chain: M
Synonym: Apc13,Cyclosome Subunit 13
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Anapc13
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Anaphase-Promoting Complex Subunit 2
Chain: N
Synonym: Apc2,Cyclosome Subunit 2
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Anapc2, Apc2, Kiaa1406
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Anaphase-Promoting Complex Subunit 5
Chain: O
Synonym: Apc5,Cyclosome Subunit 5
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Anapc5, Apc5
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Ubiquitin-Conjugating Enzyme E2 C
Chain: Q
Synonym: (E3-Independent) E2 Ubiquitin-Conjugating Enzyme C Ubiquitin-Conjugating Enzyme C,Ubch10,Ubiquitin Carrier Pro Ubiquitin-Protein Ligase C;
Ec: 2.3.2.23,2.3.2.24
Engineered: Yes
Other_details: Contains The Remnant Of A C-Terminal Linker 3c Protease Site.;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ube2c, Ubch10
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Cell Division Cycle Protein 20 Homolog
Chain: R
Synonym: P55cdc
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cdc20
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Hsl1 Peptide
Chain: S
Engineered: Yes
Other_details: Contains Azidohomoalanine In Place Of K788 A Cross-Linked To Ube2c And Ub.;
Synthetic: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Anaphase-Promoting Complex Subunit 7
Chain: X, Y
Synonym: Apc7,Cyclosome Subunit 7
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Anapc7, Apc7
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
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 6.10 Å
ligand
enzyme Transferase E.C.2.3.2.23 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


C, P


E


F, H


I


K, J


L


M


N


O


Q


R


W, G


Y, X


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (196 Kb) [Save to disk]
  • Biological Unit Coordinates (5khr.pdb1.gz) 180 Kb
  • CSU: Contacts of Structural Units for 5KHR
  • Retrieve 5KHR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5KHR from S2C, [Save to disk]
    • View 5KHR 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 5KHR
  • 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: [5khr_L] [5khr_M] [5khr_G] [5khr_Y] [5khr_K] [5khr_F] [5khr_A] [5khr_S] [5khr_C] [5khr] [5khr_J] [5khr_O] [5khr_P] [5khr_X] [5khr_N] [5khr_W] [5khr_B] [5khr_I] [5khr_Q] [5khr_H] [5khr_E] [5khr_R]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5KHR: [APC10] [APC2] [CULLIN] [RING] [TPR] [UBCc] [WD40 ] by SMART
    • Other resources with information on 5KHR
  • Community annotation for 5KHR at PDBWiki (http://pdbwiki.org)

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