1JYW

E. COLI (lacZ) BETA-GALACTOSIDASE (E537Q) IN COMPLEX WITH PNPG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.229 
  • 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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-Galactosidase
A, B, C, D
1,023Escherichia coliMutation(s): 1 
Gene Names: lacZ
EC: 3.2.1.23
UniProt
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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
147
Query on 147

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E [auth A],
ID [auth D],
OA [auth B],
XB [auth C]
4-nitrophenyl beta-D-galactopyranoside
C12 H15 N O8
IFBHRQDFSNCLOZ-YBXAARCKSA-N
DMS
Query on DMS

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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],
GC [auth C],
GD [auth C],
GE [auth D],
HA [auth A],
HB [auth B],
HC [auth C],
HD [auth C],
HE [auth D],
IA [auth A],
IB [auth B],
IC [auth C],
IE [auth D],
JA [auth A],
JB [auth B],
JC [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],
N [auth A],
NA [auth A],
NB [auth B],
NC [auth C],
NE [auth D],
O [auth A],
OB [auth B],
OC [auth C],
OE [auth D],
P [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],
RD [auth D],
RE [auth D],
S [auth A],
SB [auth B],
SC [auth C],
SD [auth D],
T [auth A],
TB [auth B],
TC [auth C],
TD [auth D],
U [auth A],
UB [auth B],
UC [auth C],
UD [auth D],
V [auth A],
VB [auth B],
VC [auth C],
VD [auth D],
W [auth A],
WA [auth B],
WB [auth B],
WC [auth C],
WD [auth D],
X [auth A],
XA [auth B],
XC [auth C],
XD [auth D],
Y [auth A],
YA [auth B],
YC [auth C],
YD [auth D],
Z [auth A],
ZA [auth B],
ZC [auth C],
ZD [auth D]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
MG
Query on MG

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AC [auth C]
F [auth A]
FC [auth C]
G [auth A]
H [auth A]
AC [auth C],
F [auth A],
FC [auth C],
G [auth A],
H [auth A],
JD [auth D],
KD [auth D],
LD [auth D],
M [auth A],
PA [auth B],
QA [auth B],
QD [auth D],
VA [auth B],
YB [auth C],
ZB [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

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BC [auth C]
CC [auth C]
DC [auth C]
EC [auth C]
I [auth A]
BC [auth C],
CC [auth C],
DC [auth C],
EC [auth C],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
MD [auth D],
ND [auth D],
OD [auth D],
PD [auth D],
RA [auth B],
SA [auth B],
TA [auth B],
UA [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.68α = 90
b = 168.6β = 90
c = 201.09γ = 90
Software Package:
Software NamePurpose
TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
TNTphasing

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