Experimental Data Snapshot

  • Resolution: 1.75 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.180 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 2.2 of the entry. See complete history


A Structural View of the Action of Escherichia Coli (Lacz) Beta-Galactosidase

Juers, D.H.Heightman, T.D.Vasella, A.McCarter, J.D.Mackenzie, L.Withers, S.G.Matthews, B.W.

(2001) Biochemistry 40: 14781-14794

  • DOI: https://doi.org/10.1021/bi011727i
  • Primary Citation of Related Structures:  
    1JYN, 1JYV, 1JYW, 1JYX, 1JZ2, 1JZ3, 1JZ4, 1JZ5, 1JZ6, 1JZ7, 1JZ8, 4V44, 4V45

  • PubMed Abstract: 

    The structures of a series of complexes designed to mimic intermediates along the reaction coordinate for beta-galactosidase are presented. These complexes clarify and enhance previous proposals regarding the catalytic mechanism. The nucleophile, Glu537, is seen to covalently bind to the galactosyl moiety. Of the two potential acids, Mg(2+) and Glu461, the latter is in better position to directly assist in leaving group departure, suggesting that the metal ion acts in a secondary role. A sodium ion plays a part in substrate binding by directly ligating the galactosyl 6-hydroxyl. The proposed reaction coordinate involves the movement of the galactosyl moiety deep into the active site pocket. For those ligands that do bind deeply there is an associated conformational change in which residues within loop 794-804 move up to 10 A closer to the site of binding. In some cases this can be inhibited by the binding of additional ligands. The resulting restricted access to the intermediate helps to explain why allolactose, the natural inducer for the lac operon, is the preferred product of transglycosylation.

  • Organizational Affiliation

    Institute of Molecular Biology, Howard Hughes Medical Institute and Department of Physics, University of Oregon, Eugene, Oregon 97403-1229, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
1,023Escherichia coliMutation(s): 1 
Gene Names: lacZ
Find proteins for P00722 (Escherichia coli (strain K12))
Explore P00722 
Go to UniProtKB:  P00722
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00722
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 145

Download Ideal Coordinates CCD File 
HC [auth C]
IC [auth C]
N [auth A]
O [auth A]
SD [auth D]
HC [auth C],
IC [auth C],
N [auth A],
O [auth A],
SD [auth D],
TD [auth D],
YA [auth B],
ZA [auth B]
2-nitrophenyl beta-D-galactopyranoside
C12 H15 N O8
Query on DMS

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth B]
AD [auth C]
AE [auth D]
BA [auth A]
AA [auth A],
AB [auth B],
AD [auth C],
AE [auth D],
BA [auth A],
BB [auth B],
BD [auth C],
BE [auth D],
CA [auth A],
CB [auth B],
CD [auth C],
CE [auth D],
DA [auth A],
DB [auth B],
DD [auth C],
DE [auth D],
EA [auth A],
EB [auth B],
ED [auth C],
EE [auth D],
FA [auth A],
FB [auth B],
FD [auth C],
FE [auth D],
GA [auth A],
GB [auth B],
GD [auth C],
GE [auth D],
HA [auth A],
HB [auth B],
HD [auth C],
HE [auth D],
IA [auth A],
IB [auth B],
ID [auth C],
IE [auth D],
JA [auth A],
JB [auth B],
JC [auth C],
JD [auth C],
JE [auth D],
KA [auth A],
KB [auth B],
KC [auth C],
KE [auth D],
LA [auth A],
LB [auth B],
LC [auth C],
LE [auth D],
MA [auth A],
MB [auth B],
MC [auth C],
ME [auth D],
NA [auth A],
NB [auth B],
NC [auth C],
NE [auth D],
OA [auth A],
OB [auth B],
OC [auth C],
OE [auth D],
P [auth A],
PA [auth A],
PB [auth B],
PC [auth C],
PE [auth D],
Q [auth A],
QB [auth B],
QC [auth C],
QE [auth D],
R [auth A],
RB [auth B],
RC [auth C],
RE [auth D],
S [auth A],
SB [auth B],
SC [auth C],
SE [auth D],
T [auth A],
TB [auth B],
TC [auth C],
TE [auth D],
U [auth A],
UB [auth B],
UC [auth C],
UD [auth D],
UE [auth D],
V [auth A],
VB [auth B],
VC [auth C],
VD [auth D],
VE [auth D],
W [auth A],
WB [auth B],
WC [auth C],
WD [auth D],
X [auth A],
XB [auth B],
XC [auth C],
XD [auth D],
Y [auth A],
YB [auth B],
YC [auth C],
YD [auth D],
Z [auth A],
ZC [auth C],
ZD [auth D]
C2 H6 O S
Query on MG

Download Ideal Coordinates CCD File 
AC [auth C]
BC [auth C]
CC [auth C]
E [auth A]
F [auth A]
AC [auth C],
BC [auth C],
CC [auth C],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
KD [auth D],
LD [auth D],
MD [auth D],
ND [auth D],
QA [auth B],
RA [auth B],
SA [auth B],
TA [auth B],
ZB [auth C]
Query on NA

Download Ideal Coordinates CCD File 
DC [auth C]
EC [auth C]
FC [auth C]
GC [auth C]
J [auth A]
DC [auth C],
EC [auth C],
FC [auth C],
GC [auth C],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
OD [auth D],
PD [auth D],
QD [auth D],
RD [auth D],
UA [auth B],
VA [auth B],
WA [auth B],
XA [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.75 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.492α = 90
b = 167.455β = 90
c = 200.341γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-12-07
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2021-10-27
    Changes: Database references, Structure summary
  • Version 2.2: 2023-08-16
    Changes: Data collection, Refinement description