PDB entry 3b6b
View 3b6b on RCSB PDB site
Description: Crystal structure of Acanthamoeba polyphaga mimivirus nucleoside diphosphate kinase complexed with dGDP
Class: transferase
Keywords: NDK, PHOSPHOTRANSFERASE, NUCLEOTIDE BINDING PROTEIN, ATP-binding, Kinase, Magnesium, Metal-binding, Nucleotide metabolism, Nucleotide-binding, Phosphorylation
Deposited on
2007-10-28, released
2008-11-04
The last revision prior to the SCOPe 2.03 freeze date was dated
2009-07-07, with a file datestamp of
2009-07-02.
Experiment type: XRAY
Resolution: 2 Å
R-factor: 0.201
AEROSPACI score: 0.44
(click here for full SPACI score report)
Chains and heterogens:
- Chain 'A':
Compound: Nucleoside diphosphate kinase
Species: Acanthamoeba polyphaga mimivirus [TaxId:212035]
Gene: ndk
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.03: d3b6ba_ - Chain 'B':
Compound: Nucleoside diphosphate kinase
Species: Acanthamoeba polyphaga mimivirus [TaxId:212035]
Gene: ndk
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.03: d3b6bb_ - Chain 'C':
Compound: Nucleoside diphosphate kinase
Species: Acanthamoeba polyphaga mimivirus [TaxId:212035]
Gene: ndk
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.03: d3b6bc_ - Chain 'D':
Compound: Nucleoside diphosphate kinase
Species: Acanthamoeba polyphaga mimivirus [TaxId:212035]
Gene: ndk
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.03: d3b6bd_ - Chain 'E':
Compound: Nucleoside diphosphate kinase
Species: Acanthamoeba polyphaga mimivirus [TaxId:212035]
Gene: ndk
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.03: d3b6be_ - Chain 'F':
Compound: Nucleoside diphosphate kinase
Species: Acanthamoeba polyphaga mimivirus [TaxId:212035]
Gene: ndk
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.03: d3b6bf_ - Heterogens: MG, DGI, HOH
PDB Chain Sequences:
- Chain 'A':
Sequence, based on SEQRES records: (download)
>3b6bA (A:)
syyhhhhhhlestslykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwsk
aprnlieqhykehseqsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirg
dlandirenlihasdsedsavdeisiwfpetkmetdn
Sequence, based on observed residues (ATOM records): (download)
>3b6bA (A:)
glqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyf
ndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdseds
avdeisiwfpe
- Chain 'B':
Sequence, based on SEQRES records: (download)
>3b6bB (B:)
syyhhhhhhlestslykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwsk
aprnlieqhykehseqsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirg
dlandirenlihasdsedsavdeisiwfpetkmetdn
Sequence, based on observed residues (ATOM records): (download)
>3b6bB (B:)
lqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyfn
dncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdsedsa
vdeisiwfp
- Chain 'C':
Sequence, based on SEQRES records: (download)
>3b6bC (C:)
syyhhhhhhlestslykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwsk
aprnlieqhykehseqsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirg
dlandirenlihasdsedsavdeisiwfpetkmetdn
Sequence, based on observed residues (ATOM records): (download)
>3b6bC (C:)
glqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyf
ndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdseds
avdeisiwfpet
- Chain 'D':
Sequence, based on SEQRES records: (download)
>3b6bD (D:)
syyhhhhhhlestslykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwsk
aprnlieqhykehseqsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirg
dlandirenlihasdsedsavdeisiwfpetkmetdn
Sequence, based on observed residues (ATOM records): (download)
>3b6bD (D:)
glqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyf
ndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdseds
avdeisiwfpe
- Chain 'E':
Sequence, based on SEQRES records: (download)
>3b6bE (E:)
syyhhhhhhlestslykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwsk
aprnlieqhykehseqsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirg
dlandirenlihasdsedsavdeisiwfpetkmetdn
Sequence, based on observed residues (ATOM records): (download)
>3b6bE (E:)
glqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyf
ndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdseds
avdeisiwfpe
- Chain 'F':
Sequence, based on SEQRES records: (download)
>3b6bF (F:)
syyhhhhhhlestslykkaglqrtlvlikpdaferslvaeimgriekknfkivsmkfwsk
aprnlieqhykehseqsyfndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirg
dlandirenlihasdsedsavdeisiwfpetkmetdn
Sequence, based on observed residues (ATOM records): (download)
>3b6bF (F:)
glqrtlvlikpdaferslvaeimgriekknfkivsmkfwskaprnlieqhykehseqsyf
ndncdfmvsgpiisivyegtdaiskirrlqgniltpgtirgdlandirenlihasdseds
avdeisiwfp