4GWM

Crystal structure of human promeprin beta


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.188
  • R-Value Work: 0.168

Literature

Macromolecules
Sequence Display for 4GWM

Classification: HYDROLASE

Total Structure Weight: 144540.16

Macromolecule Entities
Molecule Chains Length Organism Details
Meprin A subunit beta A, B 592 Homo sapiens EC#: 3.4.24.63 IUBMB
Fragment: Promeprin beta ectomoiety, UNP residues 23-614
Mutation: T23P, P24W
Gene Name(s): MEP1B Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: mpstruc | Group: MONOTOPIC MEMBRANE PROTEINS

Subgroup Name: Peptidases

Protein Name: Meprin β sheddase (metalloproteinase), pro-form


Small Molecules
Ligands 8 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

A, B N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

A, B ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

A, B BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FUC
Query on FUC

A, B ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, B SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.188
  • R-Value Work: 0.168
  • Space Group: P 1

Unit Cell:

Length (Å) Angle (°)
a = 69.62 α = 74.87
b = 71.12 β = 80.08
c = 85.74 γ = 65.13

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-09-03
  • Released Date: 2012-09-19
  • Deposition author(s): Arolas, J.L., Broder, C., Jefferson, T., Guevara, T., Sterchi, E.E., Bode, W., Stocker, W., Becker-Pauly, C., Gomis-Ruth, F.X.

Revision History

  • Version 1_0: 2012-09-19

    Type: Initial release

  • Version 1_1: 2012-10-31

    Type: Database references

  • Version 1_2: 2017-11-15

    Type: Refinement description