8VH8

Crystal structure of heparosan synthase 2 from Pasteurella multocida at 2.85 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Structural and Functional Analysis of Heparosan Synthase 2 from Pasteurella multocida to Improve the Synthesis of Heparin

Stancanelli, E.Krahn, J.A.Viverette, E.Dutcher, R.Pagadala, V.Borgnia, M.J.Liu, J.Pedersen, L.C.

(2024) ACS Catal 14: 6577-6588


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heparosan synthase B
A, B, C, D
552Pasteurella multocidaMutation(s): 0 
Gene Names: hssB
UniProt
Find proteins for Q5SGE1 (Pasteurella multocida)
Explore Q5SGE1 
Go to UniProtKB:  Q5SGE1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SGE1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UDP (Subject of Investigation/LOI)
Query on UDP

Download Ideal Coordinates CCD File 
BA [auth C]
F [auth A]
H [auth A]
MA [auth D]
N [auth B]
BA [auth C],
F [auth A],
H [auth A],
MA [auth D],
N [auth B],
OA [auth D],
P [auth B],
Z [auth C]
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
DA [auth C],
QA [auth D],
R [auth B],
X [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
AA [auth C]
E [auth A]
G [auth A]
LA [auth D]
M [auth B]
AA [auth C],
E [auth A],
G [auth A],
LA [auth D],
M [auth B],
NA [auth D],
O [auth B],
Y [auth C]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
T [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
EA [auth C]
FA [auth C]
GA [auth C]
HA [auth C]
IA [auth C]
EA [auth C],
FA [auth C],
GA [auth C],
HA [auth C],
IA [auth C],
J [auth A],
JA [auth C],
K [auth A],
KA [auth C],
L [auth A],
RA [auth D],
S [auth B],
SA [auth D],
TA [auth D],
U [auth B],
UA [auth D],
V [auth B],
W [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
CA [auth C],
I [auth A],
PA [auth D],
Q [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.57α = 90
b = 118.57β = 90
c = 262.356γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesZIC-ES102645
Department of Health & Human Services (HHS)United StatesR44GM142304
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United States1R01HL094463-09

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-04
    Type: Initial release