PDB entry 2b8q
View 2b8q on RCSB PDB site
Description: X-ray structure of Acanthamoeba ployphaga mimivirus nucleoside diphosphate kinase complexed with TDP
Class: transferase
Keywords: NDK, TDP, phosphotranferase, TRANSFERASE
Deposited on
2005-10-10, released
2005-11-15
The last revision prior to the SCOPe 2.06 freeze date was dated
2009-08-25, with a file datestamp of
2009-08-21.
Experiment type: XRAY
Resolution: 2.5 Å
R-factor: 0.199
AEROSPACI score: 0.32
(click here for full SPACI score report)
Chains and heterogens:
- Chain 'A':
Compound: Probable nucleoside diphosphate kinase
Species: Mimivirus [TaxId:315393]
Gene: ndk
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.06: d2b8qa1, d2b8qa2 - Chain 'B':
Compound: Probable nucleoside diphosphate kinase
Species: Mimivirus [TaxId:315393]
Gene: ndk
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.06: d2b8qb1, d2b8qb2 - Chain 'C':
Compound: Probable nucleoside diphosphate kinase
Species: Mimivirus [TaxId:315393]
Gene: ndk
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.06: d2b8qc1, d2b8qc2 - Chain 'D':
Compound: Probable nucleoside diphosphate kinase
Species: Mimivirus [TaxId:315393]
Gene: ndk
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.06: d2b8qd1, d2b8qd2 - Chain 'E':
Compound: Probable nucleoside diphosphate kinase
Species: Mimivirus [TaxId:315393]
Gene: ndk
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.06: d2b8qe1, d2b8qe2 - Chain 'F':
Compound: Probable nucleoside diphosphate kinase
Species: Mimivirus [TaxId:315393]
Gene: ndk
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.06: d2b8qf1, d2b8qf2 - Heterogens: MG, PO4, TYD, HOH
PDB Chain Sequences:
- Chain 'A':
Sequence, based on SEQRES records: (download)
>2b8qA (A:)
ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
qsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasd
sedsavdeisiwfpetkmetdn
Sequence, based on observed residues (ATOM records): (download)
>2b8qA (A:)
aglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsy
fndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdsed
savdeisiwfpet
- Chain 'B':
Sequence, based on SEQRES records: (download)
>2b8qB (B:)
ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
qsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasd
sedsavdeisiwfpetkmetdn
Sequence, based on observed residues (ATOM records): (download)
>2b8qB (B:)
lqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyfn
dncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdsedsa
vdeisiwfpe
- Chain 'C':
Sequence, based on SEQRES records: (download)
>2b8qC (C:)
ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
qsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasd
sedsavdeisiwfpetkmetdn
Sequence, based on observed residues (ATOM records): (download)
>2b8qC (C:)
glqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyf
ndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdseds
avdeisiwfpet
- Chain 'D':
Sequence, based on SEQRES records: (download)
>2b8qD (D:)
ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
qsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasd
sedsavdeisiwfpetkmetdn
Sequence, based on observed residues (ATOM records): (download)
>2b8qD (D:)
glqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyf
ndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdseds
avdeisiwfpet
- Chain 'E':
Sequence, based on SEQRES records: (download)
>2b8qE (E:)
ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
qsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasd
sedsavdeisiwfpetkmetdn
Sequence, based on observed residues (ATOM records): (download)
>2b8qE (E:)
glqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyf
ndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdseds
avdeisiwfpet
- Chain 'F':
Sequence, based on SEQRES records: (download)
>2b8qF (F:)
ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
qsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasd
sedsavdeisiwfpetkmetdn
Sequence, based on observed residues (ATOM records): (download)
>2b8qF (F:)
glqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyf
ndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdseds
avdeisiwfp