3MV0

E. COLI (lacZ) BETA-GALACTOSIDASE (R599A) IN COMPLEX WITH D-GALCTOPYRANOSYL-1-ONE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.195 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Importance of Arg-599 of b-galactosidase (Escherichia coli) as an anchor for the open conformations of Phe-601 and the active-site loop

Dugdale, M.L.Vance, M.L.Wheatley, R.W.Driedger, M.R.Nibber, A.Tran, A.Huber, R.E.

(2010) Biochem Cell Biol 88: 969-979


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-galactosidaseA [auth 1],
B [auth 2],
C [auth 3],
D [auth 4]
1,052Escherichia coli K-12Mutation(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
149
Query on 149

Download Ideal Coordinates CCD File 
BC [auth 3],
E [auth 1],
NA [auth 2],
QD [auth 4]
D-galactonolactone
C6 H10 O6
PHOQVHQSTUBQQK-MGCNEYSASA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
AA [auth 1]
AB [auth 2]
AC [auth 3]
AD [auth 3]
AE [auth 4]
AA [auth 1],
AB [auth 2],
AC [auth 3],
AD [auth 3],
AE [auth 4],
AF [auth 4],
BA [auth 1],
BB [auth 2],
BD [auth 3],
BE [auth 4],
CA [auth 1],
CB [auth 2],
CD [auth 3],
CE [auth 4],
DA [auth 1],
DB [auth 2],
DD [auth 3],
DE [auth 4],
EA [auth 1],
EB [auth 2],
ED [auth 3],
EE [auth 4],
FA [auth 1],
FB [auth 2],
FD [auth 3],
FE [auth 4],
GA [auth 1],
GB [auth 2],
GD [auth 3],
GE [auth 4],
HA [auth 1],
HB [auth 2],
HD [auth 3],
HE [auth 4],
IA [auth 1],
IB [auth 2],
ID [auth 3],
IE [auth 4],
JA [auth 1],
JB [auth 2],
JC [auth 3],
JD [auth 3],
JE [auth 4],
KA [auth 1],
KB [auth 2],
KC [auth 3],
KD [auth 3],
KE [auth 4],
L [auth 1],
LA [auth 1],
LB [auth 2],
LC [auth 3],
LD [auth 3],
LE [auth 4],
M [auth 1],
MA [auth 1],
MB [auth 2],
MC [auth 3],
MD [auth 3],
ME [auth 4],
N [auth 1],
NB [auth 2],
NC [auth 3],
ND [auth 3],
NE [auth 4],
O [auth 1],
OB [auth 2],
OC [auth 3],
OD [auth 3],
OE [auth 4],
P [auth 1],
PB [auth 2],
PC [auth 3],
PD [auth 3],
PE [auth 4],
Q [auth 1],
QB [auth 2],
QC [auth 3],
QE [auth 4],
R [auth 1],
RB [auth 2],
RC [auth 3],
RE [auth 4],
S [auth 1],
SB [auth 2],
SC [auth 3],
SE [auth 4],
T [auth 1],
TB [auth 2],
TC [auth 3],
TE [auth 4],
U [auth 1],
UB [auth 2],
UC [auth 3],
UE [auth 4],
V [auth 1],
VA [auth 2],
VB [auth 2],
VC [auth 3],
VE [auth 4],
W [auth 1],
WA [auth 2],
WB [auth 2],
WC [auth 3],
WE [auth 4],
X [auth 1],
XA [auth 2],
XB [auth 2],
XC [auth 3],
XE [auth 4],
Y [auth 1],
YA [auth 2],
YB [auth 2],
YC [auth 3],
YD [auth 4],
YE [auth 4],
Z [auth 1],
ZA [auth 2],
ZB [auth 2],
ZC [auth 3],
ZD [auth 4],
ZE [auth 4]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
CC [auth 3]
DC [auth 3]
EC [auth 3]
F [auth 1]
G [auth 1]
CC [auth 3],
DC [auth 3],
EC [auth 3],
F [auth 1],
G [auth 1],
OA [auth 2],
PA [auth 2],
QA [auth 2],
RD [auth 4],
SD [auth 4],
TD [auth 4]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
FC [auth 3]
GC [auth 3]
H [auth 1]
HC [auth 3]
I [auth 1]
FC [auth 3],
GC [auth 3],
H [auth 1],
HC [auth 3],
I [auth 1],
IC [auth 3],
J [auth 1],
K [auth 1],
RA [auth 2],
SA [auth 2],
TA [auth 2],
UA [auth 2],
UD [auth 4],
VD [auth 4],
WD [auth 4],
XD [auth 4]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
149 PDBBind:  3MV0 Ki: 1.40e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.84α = 90
b = 166.31β = 90
c = 201.71γ = 90
Software Package:
Software NamePurpose
CNSrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Structure summary
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-09-06
    Changes: Data collection, Database references, Refinement description