4NS1

Crystal structure of purine nucleoside phosphorylase from Porphyromonas gingivalis ATCC 33277, NYSGRC Target 30972


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Crystal structure of purine nucleoside phosphorylase from Porphyromonas gingivalis ATCC 33277, NYSGRC Target 30972.

Malashkevich, V.N.Bhosle, R.Toro, R.Hillerich, B.Gizzi, A.Garforth, S.Kar, A.Chan, M.K.Lafluer, J.Patel, H.Matikainen, B.Chamala, S.Lim, S.Celikgil, A.Villegas, G.Evans, B.Love, J.Fiser, A.Seidel, R.Bonanno, J.B.Almo, S.C.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Purine nucleoside phosphorylaseA, B, C, D295Porphyromonas gingivalis ATCC 33277Mutation(s): 0 
Gene Names: PGN_1412
EC: 2.4.2.1
UniProt
Find proteins for B2RKN6 (Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561))
Explore B2RKN6 
Go to UniProtKB:  B2RKN6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2RKN6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DA
Query on DA

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B],
P [auth C],
U [auth D]
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O6 P
KHWCHTKSEGGWEX-RRKCRQDMSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A],
J [auth A],
L [auth B],
Q [auth C],
V [auth D],
F [auth A],
J [auth A],
L [auth B],
Q [auth C],
V [auth D],
W [auth D],
X [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A],
M [auth B],
N [auth B],
G [auth A],
H [auth A],
I [auth A],
M [auth B],
N [auth B],
O [auth B],
R [auth C],
S [auth C],
T [auth C],
Y [auth D],
Z [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A, B, C, D L-PEPTIDE LINKINGC3 H7 N O3 SCYS
MSE
Query on MSE
A, B, C, D L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 218.904α = 90
b = 218.904β = 90
c = 218.904γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-3000data reduction

Structure Validation

View Full Validation Report



Entry History