4EKQ

T4 Lysozyme L99A/M102H with 4-Nitrophenol Bound

Structural Biology Knowledgebase: 4EKQ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.204
  • R-Value Work: 0.175

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4EKQ

Classification: HYDROLASE

Total Structure Weight: 44076.33

Macromolecule Entities
Molecule Chains Length Organism Details
Lysozyme A, B 187 Enterobacteria phage t4 sensu lato EC#: 3.2.1.17 IUBMB
Mutation: T21C, S38D, L99A, M102H, E108V, S117V, T142C, N144D
Gene Name(s): E

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
HED
Query on HED

A 2-HYDROXYETHYL DISULFIDE
C4 H10 O2 S2
KYNFOMQIXZUKRK-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NPO
Query on NPO

A, B P-NITROPHENOL
C6 H5 N O3
BTJIUGUIPKRLHP-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

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

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

B ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
NPO N/A in BindingDB
Kd: 2000 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.204
  • R-Value Work: 0.175
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 48.21 α = 90.00
b = 76.07 β = 93.01
c = 52.81 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-04-09
  • Released Date: 2012-09-05
  • Deposition author(s): Merski, M., Shoichet, B.K.

Revision History

  • 2012-10-17
    Type: Citation | Details: Citation update
  • 2012-10-03
    Type: Citation | Details: Citation update