PDB entry 2dxd
View 2dxd on RCSB PDB site
Description: Crystal structure of nucleoside diphosphate kinase in complex with ATP analog
Class: transferase
Keywords: nucleoside binding, kinase, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI
Deposited on
2006-08-25, released
2007-02-25
The last revision prior to the SCOP 1.75 freeze date was dated
2007-02-25, with a file datestamp of
2007-06-04.
Experiment type: XRAY
Resolution: 1.77 Å
R-factor: 0.169
AEROSPACI score: 0.68
(click here for full SPACI score report)
Chains and heterogens:
- Chain 'A':
Compound: Nucleoside diphosphate kinase
Species: Pyrococcus horikoshii
Gene: ndk
Database cross-references and differences (RAF-indexed):
Domains in SCOP 1.75: d2dxda1 - Chain 'B':
Compound: Nucleoside diphosphate kinase
Species: Pyrococcus horikoshii
Gene: ndk
Database cross-references and differences (RAF-indexed):
Domains in SCOP 1.75: d2dxdb1 - Heterogens: CL, ANP, HOH
PDB Chain Sequences:
- Chain 'A':
Sequence, based on SEQRES records: (download)
>2dxdA (A:)
mfqmsetertlviikpdavvrgligeiisrfekkglkivgmkmiwidrelaekhyeehre
kpffkalidyitktpvvvmvlegryavevvrkmagatdpkdaapgtirgdfglevsdaic
nvihasdskesaereislffkpeelfeypraadwfykkgi
Sequence, based on observed residues (ATOM records): (download)
>2dxdA (A:)
setertlviikpdavvrgligeiisrfekkglkivgmkmiwidrelaekhyeehrekpff
kalidyitktpvvvmvlegryavevvrkmagatdpkdaapgtirgdfglevsdaicnvih
asdskesaereislffkpeelfeypraadwfykk
- Chain 'B':
Sequence, based on SEQRES records: (download)
>2dxdB (B:)
mfqmsetertlviikpdavvrgligeiisrfekkglkivgmkmiwidrelaekhyeehre
kpffkalidyitktpvvvmvlegryavevvrkmagatdpkdaapgtirgdfglevsdaic
nvihasdskesaereislffkpeelfeypraadwfykkgi
Sequence, based on observed residues (ATOM records): (download)
>2dxdB (B:)
setertlviikpdavvrgligeiisrfekkglkivgmkmiwidrelaekhyeehrekpff
kalidyitktpvvvmvlegryavevvrkmagatdpkdaapgtirgdfglevsdaicnvih
asdskesaereislffkpeelfeypraadwfykk