PDB entry 3gp9
View 3gp9 on RCSB PDB site
Description: Crystal structure of the Mimivirus NDK complexed with GDP
Class: transferase
Keywords: phosphotransferase nucleotide binding, ATP-binding, Kinase, Magnesium, Metal-binding, Nucleotide metabolism, Nucleotide-binding, Phosphoprotein, Transferase
Deposited on
2009-03-23, released
2009-08-11
The last revision prior to the SCOPe 2.03 freeze date was dated
2009-08-11, with a file datestamp of
2009-08-07.
Experiment type: XRAY
Resolution: 1.8 Å
R-factor: 0.19
AEROSPACI score: 0.52
(click here for full SPACI score report)
Chains and heterogens:
- Chain 'A':
Compound: Nucleoside diphosphate kinase
Species: Acanthamoeba polyphaga mimivirus [TaxId:212035]
Gene: MIMI_R418, NDK
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.03: d3gp9a_ - Chain 'B':
Compound: Nucleoside diphosphate kinase
Species: Acanthamoeba polyphaga mimivirus [TaxId:212035]
Gene: MIMI_R418, NDK
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.03: d3gp9b_ - Chain 'C':
Compound: Nucleoside diphosphate kinase
Species: Acanthamoeba polyphaga mimivirus [TaxId:212035]
Gene: MIMI_R418, NDK
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.03: d3gp9c_ - Chain 'D':
Compound: Nucleoside diphosphate kinase
Species: Acanthamoeba polyphaga mimivirus [TaxId:212035]
Gene: MIMI_R418, NDK
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.03: d3gp9d_ - Chain 'E':
Compound: Nucleoside diphosphate kinase
Species: Acanthamoeba polyphaga mimivirus [TaxId:212035]
Gene: MIMI_R418, NDK
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.03: d3gp9e_ - Chain 'F':
Compound: Nucleoside diphosphate kinase
Species: Acanthamoeba polyphaga mimivirus [TaxId:212035]
Gene: MIMI_R418, NDK
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.03: d3gp9f_ - Heterogens: GDP, PO4, MG, HOH
PDB Chain Sequences:
- Chain 'A':
Sequence, based on SEQRES records: (download)
>3gp9A (A:)
ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
qsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasd
sedsavdeisiwfpetkmetdn
Sequence, based on observed residues (ATOM records): (download)
>3gp9A (A:)
aglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsy
fndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdsed
savdeisiwfpet
- Chain 'B':
Sequence, based on SEQRES records: (download)
>3gp9B (B:)
ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
qsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasd
sedsavdeisiwfpetkmetdn
Sequence, based on observed residues (ATOM records): (download)
>3gp9B (B:)
lqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyfn
dncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdsedsa
vdeisiwfpe
- Chain 'C':
Sequence, based on SEQRES records: (download)
>3gp9C (C:)
ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
qsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasd
sedsavdeisiwfpetkmetdn
Sequence, based on observed residues (ATOM records): (download)
>3gp9C (C:)
glqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyf
ndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdseds
avdeisiwfpet
- Chain 'D':
Sequence, based on SEQRES records: (download)
>3gp9D (D:)
ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
qsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasd
sedsavdeisiwfpetkmetdn
Sequence, based on observed residues (ATOM records): (download)
>3gp9D (D:)
glqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyf
ndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdseds
avdeisiwfpe
- Chain 'E':
Sequence, based on SEQRES records: (download)
>3gp9E (E:)
ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
qsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasd
sedsavdeisiwfpetkmetdn
Sequence, based on observed residues (ATOM records): (download)
>3gp9E (E:)
glqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyf
ndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdseds
avdeisiwfpet
- Chain 'F':
Sequence, based on SEQRES records: (download)
>3gp9F (F:)
ykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehse
qsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasd
sedsavdeisiwfpetkmetdn
Sequence, based on observed residues (ATOM records): (download)
>3gp9F (F:)
glqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyf
ndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdseds
avdeisiwfp