5K7X

Fully ligated Adenylosuccinate Synthetase from Pyrococcus horikoshii OT3 with GTP, IMP and Hadacidin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of hypothetical adenylosuccinate synthetase, PH0438 from Pyrococcus horikoshii OT3

Xie, Y.Kishisita, S.Murayama, K.Shirouzu, M.Yokoyama, S.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Adenylosuccinate synthetase
A, B, C, D, E
A, B, C, D, E, F
340Pyrococcus horikoshii OT3Mutation(s): 0 
Gene Names: purAPH0438
EC: 6.3.4.4
UniProt
Find proteins for O58187 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Explore O58187 
Go to UniProtKB:  O58187
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO58187
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
AA [auth F]
G [auth A]
K [auth B]
O [auth C]
S [auth D]
AA [auth F],
G [auth A],
K [auth B],
O [auth C],
S [auth D],
W [auth E]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
IMP
Query on IMP

Download Ideal Coordinates CCD File 
BA [auth F]
H [auth A]
L [auth B]
P [auth C]
T [auth D]
BA [auth F],
H [auth A],
L [auth B],
P [auth C],
T [auth D],
X [auth E]
INOSINIC ACID
C10 H13 N4 O8 P
GRSZFWQUAKGDAV-KQYNXXCUSA-N
HDA
Query on HDA

Download Ideal Coordinates CCD File 
CA [auth F]
I [auth A]
M [auth B]
Q [auth C]
U [auth D]
CA [auth F],
I [auth A],
M [auth B],
Q [auth C],
U [auth D],
Y [auth E]
HADACIDIN
C3 H5 N O4
URJHVPKUWOUENU-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
DA [auth F]
J [auth A]
N [auth B]
R [auth C]
V [auth D]
DA [auth F],
J [auth A],
N [auth B],
R [auth C],
V [auth D],
Z [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.348α = 90
b = 130.549β = 90
c = 168.673γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina81473114

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-07
    Type: Initial release
  • Version 1.1: 2017-08-16
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description