5MNJ

Structure of MDM2-MDMX-UbcH5B-ubiquitin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.190

Literature

Macromolecules
Sequence Display for 5MNJ

Classification: LIGASE

Total Structure Weight: 86014.67

Macromolecule Entities
Molecule Chains Length Organism Details
Ubiquitin-conjugating enzyme E2 D2 A, E 147 Homo sapiens EC#: 2.3.2.23 IUBMB
Mutation: S22R, C85K
Details: K85 in Chains A and E form isopeptide linkage with the carbonyl carbon of G76 in Chains B and F, respectively.
Gene Name(s): UBE2D2 Gene View PUBC1 UBC4 UBC5B UBCH4 UBCH5B
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Polyubiquitin-B B, F 81 Homo sapiens Details: gsggs linker at the N-terminus resulted from cloning. G76 in chain B is covalently linked to K85 side chain in Chain A.
Gene Name(s): UBB Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
E3 ubiquitin-protein ligase Mdm2 C, G 86 Homo sapiens EC#: 6.3.2 IUBMB
Details: Contains N-terminal His-tag followed by TEV protease cleavage site that was not removed during purification. MDM2 contains 428-491.
Gene Name(s): MDM2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Protein Mdm4 D, H 64 Homo sapiens Details: MDMX contains 427-490
Gene Name(s): MDM4 Gene View MDMX
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SO4
Query on SO4

D, H SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

C, D, G, H ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.190
  • Space Group: P 1

Unit Cell:

Length (Å) Angle (°)
a = 54.24 α = 69.83
b = 62.76 β = 69.22
c = 66.35 γ = 78.21

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-12-13
  • Released Date: 2017-05-31
  • Deposition author(s): Klejnot, M., Huang, D.T.

Revision History

  • Version 1_0: 2017-05-31

    Type: Initial release

  • Version 1_1: 2017-06-07

    Type: Database references

  • Version 1_2: 2017-07-19

    Type: Database references