5UTU

2.65 Angstrom Resolution Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with SAH and NAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

2.65 Angstrom Resolution Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with SAH and NAD

Minasov, G.Shuvalova, L.Dubrovska, I.Winsor, J.Stam, J.Kwon, K.Anderson, W.F.Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Adenosylhomocysteinase
A, B, C, D, E
A, B, C, D, E, F, G, H
498Cryptosporidium parvum Iowa IIMutation(s): 0 
Gene Names: cgd3_80
EC: 3.3.1.1
UniProt
Find proteins for Q5CPH1 (Cryptosporidium parvum (strain Iowa II))
Explore Q5CPH1 
Go to UniProtKB:  Q5CPH1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5CPH1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
EA [auth D]
HB [auth H]
I [auth A]
LA [auth E]
Q [auth B]
EA [auth D],
HB [auth H],
I [auth A],
LA [auth E],
Q [auth B],
RA [auth F],
X [auth C],
YA [auth G]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
SAH
Query on SAH

Download Ideal Coordinates CCD File 
FA [auth D]
IB [auth H]
J [auth A]
MA [auth E]
R [auth B]
FA [auth D],
IB [auth H],
J [auth A],
MA [auth E],
R [auth B],
SA [auth F],
Y [auth C],
ZA [auth G]
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
P33
Query on P33

Download Ideal Coordinates CCD File 
NB [auth H],
P [auth A],
W [auth B]
3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
C14 H30 O8
XPJRQAIZZQMSCM-UHFFFAOYSA-N
P6G
Query on P6G

Download Ideal Coordinates CCD File 
KA [auth D],
XA [auth F]
HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
ADN
Query on ADN

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JB [auth H],
TA [auth F]
ADENOSINE
C10 H13 N5 O4
OIRDTQYFTABQOQ-KQYNXXCUSA-N
PEG
Query on PEG

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FB [auth G],
GB [auth G]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CA [auth C]
CB [auth G]
DA [auth C]
AA [auth C],
BA [auth C],
CA [auth C],
CB [auth G],
DA [auth C],
DB [auth G],
EB [auth G],
HA [auth D],
IA [auth D],
JA [auth D],
L [auth A],
LB [auth H],
M [auth A],
MB [auth H],
N [auth A],
O [auth A],
PA [auth E],
QA [auth E],
U [auth B],
V [auth B],
VA [auth F],
WA [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL
Query on CL

Download Ideal Coordinates CCD File 
AB [auth G]
BB [auth G]
GA [auth D]
K [auth A]
KB [auth H]
AB [auth G],
BB [auth G],
GA [auth D],
K [auth A],
KB [auth H],
NA [auth E],
OA [auth E],
S [auth B],
T [auth B],
UA [auth F],
Z [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.906α = 90
b = 185.834β = 97.98
c = 121.619γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-01
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Refinement description, Structure summary