148L

A COVALENT ENZYME-SUBSTRATE INTERMEDIATE WITH SACCHARIDE DISTORTION IN A MUTANT T4 LYSOZYME

Structural Biology Knowledgebase: 148L SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Observed: 0.168

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 148L

Classification: HYDROLASE / HYDROLASE SUBSTRATE

Total Structure Weight: 19692.59

Macromolecule Entities
Molecule Chains Length Organism Details
T4 LYSOZYME E 164 Enterobacteria phage t4 sensu lato EC#: 3.2.1.17 IUBMB
Mutation: T26E, C54T, C97A
Gene Name(s): E
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
SUBSTRATE CLEAVED FROM CELL WALL OF ESCHERICHIA COLI S 4 Escherichia coli

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

S N-ACETYLMURAMIC ACID
C11 H19 N O8
MNLRQHMNZILYPY-MDMHTWEWSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

S N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BME
Query on BME

E BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 3 Unique
ID Chains Type Formula 2D Diagram Parent
FGA
Query on FGA
S D-gamma-peptide, C-delta linking C5 H9 N O4 --
API
Query on API
S L-PEPTIDE LINKING C7 H14 N2 O4 LYS
DAL
Query on DAL
S D-PEPTIDE LINKING C3 H7 N O2 --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Observed: 0.168
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 50.90 α = 90.00
b = 67.30 β = 90.00
c = 49.60 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1993-10-27
  • Released Date: 1994-04-30
  • Deposition author(s): Kuroki, R., Weaver, L.H., Matthews, B.W.

Revision History

  • 2011-07-27
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-27
    Type: Binding sites and description | Details: Binding sites and description
  • 2011-07-27
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-27
    Type: Function and keywords | Details: Function and keywords
  • 2011-07-27
    Type: Linkage | Details: Linkage
  • 2011-07-27
    Type: Sequence database correspondence | Details: Sequence database correspondence
  • 2011-07-27
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4