6YX8

The structure of allophycocyanin from cyanobacterium Nostoc sp. WR13, the C2221 crystal form.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.160 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

The high resolution structure of allophycocyanin from cyanobacterium Nostoc sp. WR13

Patel, H.M.Roszak, A.W.Madamwar, D.Cogdell, R.J.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ALPHA SUBUNIT OF CYANOBACTERIAL ALLOPHYCOCYANIN PROTEINA [auth AAA],
C [auth CCC],
E [auth EEE]
160Nostoc sp. WR13Mutation(s): 0 
UniProt
Find proteins for A0A4Y5PW22 (Nostoc sp. WR13)
Explore A0A4Y5PW22 
Go to UniProtKB:  A0A4Y5PW22
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4Y5PW22
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
BETA SUBUNIT OF CYANOBACTERIAL ALLOPHYCOCYANIN PROTEINB [auth BBB],
D [auth DDD],
F [auth FFF]
161Nostoc sp. WR13Mutation(s): 0 
UniProt
Find proteins for A0A4Y5PW23 (Nostoc sp. WR13)
Explore A0A4Y5PW23 
Go to UniProtKB:  A0A4Y5PW23
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4Y5PW23
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PXQ (Subject of Investigation/LOI)
Query on PXQ

Download Ideal Coordinates CCD File 
G [auth AAA]
JC [auth FFF]
OA [auth CCC]
RB [auth EEE]
W [auth BBB]
G [auth AAA],
JC [auth FFF],
OA [auth CCC],
RB [auth EEE],
W [auth BBB],
ZA [auth DDD]
3-[5-[[(3~{R},4~{R})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydropyrrol-2-yl]methyl]-2-[[5-[(~{Z})-(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{H}-pyrrol-2-yl]methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid
C33 H42 N4 O6
RIXXCMVADHNPLY-UKJJQICTSA-N
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
AA [auth BBB],
BA [auth BBB],
J [auth AAA],
MA [auth BBB],
OC [auth FFF]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
EB [auth DDD],
FB [auth DDD],
GB [auth DDD],
QB [auth EEE],
TB [auth EEE]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
BCN
Query on BCN

Download Ideal Coordinates CCD File 
DB [auth DDD],
I [auth AAA]
BICINE
C6 H13 N O4
FSVCELGFZIQNCK-UHFFFAOYSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
CA [auth BBB]
DA [auth BBB]
IC [auth EEE]
K [auth AAA]
PC [auth FFF]
CA [auth BBB],
DA [auth BBB],
IC [auth EEE],
K [auth AAA],
PC [auth FFF],
QA [auth CCC],
QC [auth FFF],
RC [auth FFF],
SC [auth FFF],
U [auth AAA],
UB [auth EEE]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
MRD
Query on MRD

Download Ideal Coordinates CCD File 
SB [auth EEE](4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
AB [auth DDD]
BB [auth DDD]
CB [auth DDD]
H [auth AAA]
KC [auth FFF]
AB [auth DDD],
BB [auth DDD],
CB [auth DDD],
H [auth AAA],
KC [auth FFF],
LC [auth FFF],
MC [auth FFF],
NC [auth FFF],
PA [auth CCC],
X [auth BBB],
Y [auth BBB],
Z [auth BBB]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
EA [auth BBB]
FA [auth BBB]
GA [auth BBB]
HB [auth DDD]
IB [auth DDD]
EA [auth BBB],
FA [auth BBB],
GA [auth BBB],
HB [auth DDD],
IB [auth DDD],
JB [auth DDD],
L [auth AAA],
M [auth AAA],
N [auth AAA],
O [auth AAA],
RA [auth CCC],
SA [auth CCC],
TA [auth CCC],
TC [auth FFF],
UA [auth CCC],
UC [auth FFF],
VB [auth EEE],
VC [auth FFF],
WB [auth EEE],
WC [auth FFF],
XA [auth CCC],
XB [auth EEE],
YB [auth EEE]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AC [auth EEE]
AD [auth FFF]
BC [auth EEE]
CC [auth EEE]
DC [auth EEE]
AC [auth EEE],
AD [auth FFF],
BC [auth EEE],
CC [auth EEE],
DC [auth EEE],
EC [auth EEE],
FC [auth EEE],
GC [auth EEE],
HA [auth BBB],
HC [auth EEE],
IA [auth BBB],
JA [auth BBB],
KA [auth BBB],
KB [auth DDD],
LA [auth BBB],
LB [auth DDD],
MB [auth DDD],
NA [auth CCC],
NB [auth DDD],
OB [auth DDD],
P [auth AAA],
PB [auth DDD],
Q [auth AAA],
R [auth AAA],
S [auth AAA],
T [auth AAA],
V [auth AAA],
VA [auth CCC],
WA [auth CCC],
XC [auth FFF],
YA [auth DDD],
YC [auth FFF],
ZB [auth EEE],
ZC [auth FFF]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MEN
Query on MEN
B [auth BBB],
D [auth DDD],
F [auth FFF]
L-PEPTIDE LINKINGC5 H10 N2 O3ASN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.160 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.676α = 90
b = 177.34β = 90
c = 122.416γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
autoPROCdata scaling
STARANISOdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-SC0001035 (Office of Basic Energy Sciences)
Department of Biotechnology (DBT, India)IndiaBT/PR15686/AAQ/3/811/2016 (UGC-BSR Faculty Fellowship)
Department of Biotechnology (DBT, India)IndiaBT/IN/UK/DBT-BC/2017-18 (Newton-Bhabha fellowship)

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-12
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description