6NDD

RHODOCETIN IN COMPLEX WITH THE INTEGRIN ALPHA2-A DOMAIN WITH MANGANESE BOUND


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

RHODOCETIN IN COMPLEX WITH THE INTEGRIN ALPHA2-A DOMAIN WITH MANGANESE BOUND

Stetefeld, J.McDougall, M.D.Loewen, P.C.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Snaclec rhodocetin subunit gamma
A, D, G, J, M
A, D, G, J, M, P
135Calloselasma rhodostomaMutation(s): 0 
UniProt
Find proteins for D2YW39 (Calloselasma rhodostoma)
Explore D2YW39 
Go to UniProtKB:  D2YW39
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD2YW39
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Snaclec rhodocetin subunit delta
B, E, H, K, N
B, E, H, K, N, Q
124Calloselasma rhodostomaMutation(s): 0 
UniProt
Find proteins for D2YW40 (Calloselasma rhodostoma)
Explore D2YW40 
Go to UniProtKB:  D2YW40
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD2YW40
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Integrin alpha-2
C, F, I, L, O
C, F, I, L, O, R
217Homo sapiensMutation(s): 0 
Gene Names: ITGA2CD49B
UniProt & NIH Common Fund Data Resources
Find proteins for P17301 (Homo sapiens)
Explore P17301 
Go to UniProtKB:  P17301
PHAROS:  P17301
GTEx:  ENSG00000164171 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17301
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth E]
AB [auth R]
DA [auth F]
GA [auth G]
JA [auth I]
AA [auth E],
AB [auth R],
DA [auth F],
GA [auth G],
JA [auth I],
LA [auth J],
OA [auth K],
S [auth A],
T [auth A],
TA [auth N],
V [auth C],
WA [auth O],
XA [auth Q],
Y [auth D],
YA [auth Q]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
MN
Query on MN

Download Ideal Coordinates CCD File 
CA [auth F]
IA [auth I]
PA [auth L]
U [auth C]
UA [auth O]
CA [auth F],
IA [auth I],
PA [auth L],
U [auth C],
UA [auth O],
ZA [auth R]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
BA [auth E]
BB [auth R]
FA [auth G]
HA [auth H]
MA [auth J]
BA [auth E],
BB [auth R],
FA [auth G],
HA [auth H],
MA [auth J],
NA [auth K],
RA [auth L],
SA [auth M],
X [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
CB [auth R]
EA [auth F]
KA [auth I]
QA [auth L]
VA [auth O]
CB [auth R],
EA [auth F],
KA [auth I],
QA [auth L],
VA [auth O],
W [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
NH4
Query on NH4

Download Ideal Coordinates CCD File 
Z [auth D]AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.712α = 90
b = 130.712β = 90
c = 251.8γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-26
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description