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2AZ3
Asym. Unit
Info
Asym.Unit (231 KB)
Biol.Unit 1 (150 KB)
Biol.Unit 2 (150 KB)
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(1)
Title
:
STRUCTURE OF A HALOPHILIC NUCLEOSIDE DIPHOSPHATE KINASE FROM HALOBACTERIUM SALINARUM IN COMPLEX WITH CDP
Authors
:
H. Besir, K. Zeth, A. Bracher, U. Heider, M. Ishibashi, M. Tokunaga, D. Oesterhelt
Date
:
09 Sep 05 (Deposition) - 20 Dec 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I
Biol. Unit 1: A,B,C (2x)
Biol. Unit 2: D,E,F,G,H,I (1x)
Keywords
:
Halophilic, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Besir, K. Zeth, A. Bracher, U. Heider, M. Ishibashi, M. Tokunaga, D. Oesterhelt
Structure Of A Halophilic Nucleoside Diphosphate Kinase From Halobacterium Salinarum
Febs Lett. V. 579 6595 2005
(for further references see the
PDB file header
)
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Hetero Components
(2, 11)
Info
All Hetero Components
1a: CYTIDINE-5'-DIPHOSPHATE (CDPa)
1b: CYTIDINE-5'-DIPHOSPHATE (CDPb)
1c: CYTIDINE-5'-DIPHOSPHATE (CDPc)
1d: CYTIDINE-5'-DIPHOSPHATE (CDPd)
1e: CYTIDINE-5'-DIPHOSPHATE (CDPe)
1f: CYTIDINE-5'-DIPHOSPHATE (CDPf)
1g: CYTIDINE-5'-DIPHOSPHATE (CDPg)
1h: CYTIDINE-5'-DIPHOSPHATE (CDPh)
1i: CYTIDINE-5'-DIPHOSPHATE (CDPi)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CDP
9
Ligand/Ion
CYTIDINE-5'-DIPHOSPHATE
2
MG
2
Ligand/Ion
MAGNESIUM ION
[
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Sites
(11, 11)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:55 , CDP A:1100
BINDING SITE FOR RESIDUE MG A 201
02
AC2
SOFTWARE
GLU B:55 , CDP B:1200
BINDING SITE FOR RESIDUE MG B 202
03
AC3
SOFTWARE
LYS A:13 , GLU A:55 , HIS A:56 , PHE A:61 , LEU A:65 , ARG A:89 , THR A:95 , LEU A:113 , GLY A:114 , ASN A:116 , HIS A:119 , MG A:201 , HOH A:1112 , HOH A:1115 , GLU D:55 , GLU D:57 , ASP D:58
BINDING SITE FOR RESIDUE CDP A 1100
04
AC4
SOFTWARE
LYS B:13 , HIS B:56 , PHE B:61 , LEU B:65 , ARG B:89 , THR B:95 , LEU B:113 , GLY B:114 , ASN B:116 , MG B:202 , GLU F:55 , GLU F:57 , ASP F:58
BINDING SITE FOR RESIDUE CDP B 1200
05
AC5
SOFTWARE
LYS C:13 , HIS C:56 , PHE C:61 , LEU C:65 , ARG C:89 , THR C:95 , LEU C:113 , GLY C:114 , ASN C:116 , HIS C:119 , HOH C:1308 , GLU E:55 , GLU E:57 , ASP E:58
BINDING SITE FOR RESIDUE CDP C 1300
06
AC6
SOFTWARE
LYS D:13 , HIS D:56 , PHE D:61 , LEU D:65 , ARG D:89 , THR D:95 , ARG D:106 , LEU D:113 , GLY D:114 , ASN D:116
BINDING SITE FOR RESIDUE CDP D 1400
07
AC7
SOFTWARE
LYS E:13 , HIS E:56 , PHE E:61 , LEU E:65 , ARG E:89 , THR E:95 , ARG E:106 , LEU E:113 , GLY E:114 , ASN E:116
BINDING SITE FOR RESIDUE CDP E 1500
08
AC8
SOFTWARE
HIS F:56 , PHE F:61 , LEU F:65 , ARG F:89 , THR F:95 , LEU F:113 , GLY F:114 , ASN F:116
BINDING SITE FOR RESIDUE CDP F 1600
09
AC9
SOFTWARE
LYS G:13 , TYR G:53 , HIS G:56 , PHE G:61 , LEU G:65 , ARG G:89 , THR G:95 , LEU G:113 , GLY G:114 , ASN G:116 , HIS G:119 , HOH G:1702
BINDING SITE FOR RESIDUE CDP G 1700
10
BC1
SOFTWARE
GLU G:124 , LYS H:13 , HIS H:56 , PHE H:61 , LEU H:65 , ARG H:89 , THR H:95 , LEU H:113 , ASN H:116 , HIS H:119 , HOH H:1816
BINDING SITE FOR RESIDUE CDP H 1800
11
BC2
SOFTWARE
LYS I:13 , HIS I:56 , PHE I:61 , LEU I:65 , ARG I:89 , THR I:95 , ARG I:106 , LEU I:113 , GLY I:114 , ASN I:116 , HIS I:119
BINDING SITE FOR RESIDUE CDP I 1900
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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Exons
(0, 0)
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 9)
Info
All SCOP Domains
1a: SCOP_d2az3a_ (A:)
1b: SCOP_d2az3b_ (B:)
1c: SCOP_d2az3c_ (C:)
1d: SCOP_d2az3d_ (D:)
1e: SCOP_d2az3e_ (E:)
1f: SCOP_d2az3f_ (F:)
1g: SCOP_d2az3g_ (G:)
1h: SCOP_d2az3h_ (H:)
1i: SCOP_d2az3i_ (I:)
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)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
Nucleoside diphosphate kinase, NDK
(129)
Family
:
Nucleoside diphosphate kinase, NDK
(112)
Protein domain
:
Nucleoside diphosphate kinase, NDK
(66)
Halobacterium salinarum [TaxId: 2242]
(2)
1a
d2az3a_
A:
1b
d2az3b_
B:
1c
d2az3c_
C:
1d
d2az3d_
D:
1e
d2az3e_
E:
1f
d2az3f_
F:
1g
d2az3g_
G:
1h
d2az3h_
H:
1i
d2az3i_
I:
[
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CATH Domains
(1, 9)
Info
all CATH domains
1a: CATH_2az3B00 (B:5-155)
1b: CATH_2az3I00 (I:5-155)
1c: CATH_2az3A00 (A:4-155)
1d: CATH_2az3D00 (D:4-155)
1e: CATH_2az3E00 (E:4-155)
1f: CATH_2az3F00 (F:4-155)
1g: CATH_2az3G00 (G:4-155)
1h: CATH_2az3H00 (H:4-155)
1i: CATH_2az3C00 (C:4-156)
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Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.141, no name defined]
(46)
Halobacterium salinarum. Organism_taxid: 2242.
(1)
1a
2az3B00
B:5-155
1b
2az3I00
I:5-155
1c
2az3A00
A:4-155
1d
2az3D00
D:4-155
1e
2az3E00
E:4-155
1f
2az3F00
F:4-155
1g
2az3G00
G:4-155
1h
2az3H00
H:4-155
1i
2az3C00
C:4-156
[
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Pfam Domains
(0, 0)
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all PFAM domains
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Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
Chain I
Asymmetric Unit 1
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select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
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set fontsize 20
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show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
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Show PDB file:
Asym.Unit (231 KB)
Header - Asym.Unit
Biol.Unit 1 (150 KB)
Header - Biol.Unit 1
Biol.Unit 2 (150 KB)
Header - Biol.Unit 2
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