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, TRANSFERASE
Deposited on
2006-08-25, released
2007-02-25
The last revision prior to the SCOPe 2.08 freeze date was dated
2021-04-28, with a file datestamp of
2021-04-23.
Experiment type: XRAY
Resolution: 1.77 Å
R-factor: N/A
AEROSPACI score: 0.47
(click here for full SPACI score report)
Chains and heterogens:
- Chain 'A':
Compound: Nucleoside diphosphate kinase
Species: Pyrococcus horikoshii [TaxId:70601]
Gene: ndk, PH0698
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.08: d2dxda_ - Chain 'B':
Compound: Nucleoside diphosphate kinase
Species: Pyrococcus horikoshii [TaxId:70601]
Gene: ndk, PH0698
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.08: d2dxdb_ - 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