3GUP

T4 lysozyme M102E/L99A mutant with buried charge in apolar cavity--pyridine binding


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.211

Literature

Macromolecules
Sequence Display for 3GUP

Classification: HYDROLASE

Total Structure Weight: 37942.57

Macromolecule Entities
Molecule Chains Length Organism Details
Lysozyme A, B 164 Escherichia virus t4 EC#: 3.2.1.17 IUBMB
Mutation: T21C, S38D, L99A, M102E, E108V, S117V, T142C, N144D
Gene Name(s): E
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
0PY
Query on 0PY

A, B pyridine
Azine, (Synonym)
C5 H5 N
JUJWROOIHBZHMG-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CO3
Query on CO3

A, B CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
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)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CME
Query on CME
A, B L-PEPTIDE LINKING C5 H11 N O3 S2 CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.211
  • Space Group: P 43

Unit Cell:

Length (Å) Angle (°)
a = 48.96 α = 90.00
b = 48.96 β = 90.00
c = 129.32 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-03-30
  • Released Date: 2009-08-25
  • Deposition author(s): Liu, L., Matthews, B.W.

Revision History

  • Version 1_0: 2009-08-25

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Advisory, Refinement description, Version format compliance

  • Version 1_2: 2017-11-01

    Type: Refinement description