3GUJ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.202

Literature

Macromolecules
Sequence Display for 3GUJ

Classification: HYDROLASE

Total Structure Weight: 19260.19

Macromolecule Entities
Molecule Chains Length Organism Details
Lysozyme A 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 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
EPE
Query on EPE

A 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES (Synonym)
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BME
Query on BME

A BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BNZ
Query on BNZ

A BENZENE
C6 H6
UHOVQNZJYSORNB-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CO3
Query on CO3

A CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
BNZ N/A in BindingDB
Ka: 37200 M-1  BindingMOAD
N/A in PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CME
Query on CME
A L-PEPTIDE LINKING C5 H11 N O3 S2 CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.202
  • Space Group: P 41 21 2

Unit Cell:

Length (Å) Angle (°)
a = 48.81 α = 90.00
b = 48.81 β = 90.00
c = 128.37 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