PDB entry 3q8v
View 3q8v on RCSB PDB site
Description: Crystal structure of Staphylococcus aureus nucleoside diphosphate kinase complexed with UDP
Class: transferase
Keywords: Ferridoxin fold, alpha-beta protein family, Nucleoside diphosphate kinases (NDKs), a gamma phosphate, nucleoside triphosphates, nucleoside diphosphate, Nucleotide binding, Magnesium, Metal binding, Phosphorylation, TRANSFERASE
Deposited on
2011-01-07, released
2011-07-27
The last revision prior to the SCOPe 2.08 freeze date was dated
2011-07-27, with a file datestamp of
2011-07-22.
Experiment type: XRAY
Resolution: 2.5 Å
R-factor: 0.233
AEROSPACI score: 0.29
(click here for full SPACI score report)
Chains and heterogens:
- Chain 'A':
Compound: Nucleoside diphosphate kinase
Species: Staphylococcus aureus subsp. aureus [TaxId:93062]
Gene: ndk, SACOL1509
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.08: d3q8va_ - Chain 'B':
Compound: Nucleoside diphosphate kinase
Species: Staphylococcus aureus subsp. aureus [TaxId:93062]
Gene: ndk, SACOL1509
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.08: d3q8vb_ - Chain 'C':
Compound: Nucleoside diphosphate kinase
Species: Staphylococcus aureus subsp. aureus [TaxId:93062]
Gene: ndk, SACOL1509
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.08: d3q8vc_ - Chain 'D':
Compound: Nucleoside diphosphate kinase
Species: Staphylococcus aureus subsp. aureus [TaxId:93062]
Gene: ndk, SACOL1509
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.08: d3q8vd_ - Chain 'E':
Compound: Nucleoside diphosphate kinase
Species: Staphylococcus aureus subsp. aureus [TaxId:93062]
Gene: ndk, SACOL1509
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.08: d3q8ve_ - Chain 'F':
Compound: Nucleoside diphosphate kinase
Species: Staphylococcus aureus subsp. aureus [TaxId:93062]
Gene: ndk, SACOL1509
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.08: d3q8vf_ - Chain 'G':
Compound: Nucleoside diphosphate kinase
Species: Staphylococcus aureus subsp. aureus [TaxId:93062]
Gene: ndk, SACOL1509
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.08: d3q8vg_ - Chain 'H':
Compound: Nucleoside diphosphate kinase
Species: Staphylococcus aureus subsp. aureus [TaxId:93062]
Gene: ndk, SACOL1509
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.08: d3q8vh_ - Heterogens: UDP, MG, HOH
PDB Chain Sequences:
- Chain 'A':
Sequence, based on SEQRES records: (download)
>3q8vA (A:)
mertflmikpdavqrnligevisrierkglklvggklmqvpmelaethygehqgkpfynd
lisfitsapvfamvvegedavnvsrhiigstnpseaspgsirgdlgltvgrniihgsdsl
esaereinlwfneneitsyasprdawlyelehhhhhh
Sequence, based on observed residues (ATOM records): (download)
>3q8vA (A:)
mertflmikpdavqrnligevisrierkglklvggklmqvpmelaethygehqgkpfynd
lisfitsapvfamvvegedavnvsrhiigstnpseaspgsirgdlgltvgrniihgsdsl
esaereinlwfneneitsyasprdawlye
- Chain 'B':
Sequence, based on SEQRES records: (download)
>3q8vB (B:)
mertflmikpdavqrnligevisrierkglklvggklmqvpmelaethygehqgkpfynd
lisfitsapvfamvvegedavnvsrhiigstnpseaspgsirgdlgltvgrniihgsdsl
esaereinlwfneneitsyasprdawlyelehhhhhh
Sequence, based on observed residues (ATOM records): (download)
>3q8vB (B:)
mertflmikpdavqrnligevisrierkglklvggklmqvpmelaethygehqgkpfynd
lisfitsapvfamvvegedavnvsrhiigstnpseaspgsirgdlgltvgrniihgsdsl
esaereinlwfneneitsyasprdawlye
- Chain 'C':
Sequence, based on SEQRES records: (download)
>3q8vC (C:)
mertflmikpdavqrnligevisrierkglklvggklmqvpmelaethygehqgkpfynd
lisfitsapvfamvvegedavnvsrhiigstnpseaspgsirgdlgltvgrniihgsdsl
esaereinlwfneneitsyasprdawlyelehhhhhh
Sequence, based on observed residues (ATOM records): (download)
>3q8vC (C:)
mertflmikpdavqrnligevisrierkglklvggklmqvpmelaethygehqgkpfynd
lisfitsapvfamvvegedavnvsrhiigstnpseaspgsirgdlgltvgrniihgsdsl
esaereinlwfneneitsyasprdawlye
- Chain 'D':
Sequence, based on SEQRES records: (download)
>3q8vD (D:)
mertflmikpdavqrnligevisrierkglklvggklmqvpmelaethygehqgkpfynd
lisfitsapvfamvvegedavnvsrhiigstnpseaspgsirgdlgltvgrniihgsdsl
esaereinlwfneneitsyasprdawlyelehhhhhh
Sequence, based on observed residues (ATOM records): (download)
>3q8vD (D:)
mertflmikpdavqrnligevisrierkglklvggklmqvpmelaethygehqgkpfynd
lisfitsapvfamvvegedavnvsrhiigstnpseaspgsirgdlgltvgrniihgsdsl
esaereinlwfneneitsyasprdawlye
- Chain 'E':
Sequence, based on SEQRES records: (download)
>3q8vE (E:)
mertflmikpdavqrnligevisrierkglklvggklmqvpmelaethygehqgkpfynd
lisfitsapvfamvvegedavnvsrhiigstnpseaspgsirgdlgltvgrniihgsdsl
esaereinlwfneneitsyasprdawlyelehhhhhh
Sequence, based on observed residues (ATOM records): (download)
>3q8vE (E:)
mertflmikpdavqrnligevisrierkglklvggklmqvpmelaethygehqgkpfynd
lisfitsapvfamvvegedavnvsrhiigstnpseaspgsirgdlgltvgrniihgsdsl
esaereinlwfneneitsyasprdawlye
- Chain 'F':
Sequence, based on SEQRES records: (download)
>3q8vF (F:)
mertflmikpdavqrnligevisrierkglklvggklmqvpmelaethygehqgkpfynd
lisfitsapvfamvvegedavnvsrhiigstnpseaspgsirgdlgltvgrniihgsdsl
esaereinlwfneneitsyasprdawlyelehhhhhh
Sequence, based on observed residues (ATOM records): (download)
>3q8vF (F:)
mertflmikpdavqrnligevisrierkglklvggklmqvpmelaethygehqgkpfynd
lisfitsapvfamvvegedavnvsrhiigstnpseaspgsirgdlgltvgrniihgsdsl
esaereinlwfneneitsyasprdawlye
- Chain 'G':
Sequence, based on SEQRES records: (download)
>3q8vG (G:)
mertflmikpdavqrnligevisrierkglklvggklmqvpmelaethygehqgkpfynd
lisfitsapvfamvvegedavnvsrhiigstnpseaspgsirgdlgltvgrniihgsdsl
esaereinlwfneneitsyasprdawlyelehhhhhh
Sequence, based on observed residues (ATOM records): (download)
>3q8vG (G:)
mertflmikpdavqrnligevisrierkglklvggklmqvpmelaethygehqgkpfynd
lisfitsapvfamvvegedavnvsrhiigstnpseaspgsirgdlgltvgrniihgsdsl
esaereinlwfneneitsyasprdawlye
- Chain 'H':
Sequence, based on SEQRES records: (download)
>3q8vH (H:)
mertflmikpdavqrnligevisrierkglklvggklmqvpmelaethygehqgkpfynd
lisfitsapvfamvvegedavnvsrhiigstnpseaspgsirgdlgltvgrniihgsdsl
esaereinlwfneneitsyasprdawlyelehhhhhh
Sequence, based on observed residues (ATOM records): (download)
>3q8vH (H:)
mertflmikpdavqrnligevisrierkglklvggklmqvpmelaethygehqgkpfynd
lisfitsapvfamvvegedavnvsrhiigstnpseaspgsirgdlgltvgrniihgsdsl
esaereinlwfneneitsyasprdawlye