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2BEF
Biol. Unit 1
Info
Asym.Unit (83 KB)
Biol.Unit 1 (153 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF NDP KINASE COMPLEXED WITH MG, ADP, AND BEF3
Authors
:
Y. W. Xu, J. Cherfils
Date
:
26 May 98 (Deposition) - 12 Aug 98 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (2x)
Keywords
:
Phosphotransferase, Nucleoside Diphosphate Kinase, Phosphoryl Transfer, Beryllium Fluoride
(Keyword Search:
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)
Reference
:
Y. W. Xu, S. Morera, J. Janin, J. Cherfils
Alf3 Mimics The Transition State Of Protein Phosphorylation In The Crystal Structure Of Nucleoside Diphosphate Kinase And Mgadp.
Proc. Natl. Acad. Sci. Usa V. 94 3579 1997
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Hetero Components
(2, 12)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
1b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
1c: ADENOSINE-5'-DIPHOSPHATE (ADPc)
2a: BERYLLIUM TRIFLUORIDE ION (BEFa)
2b: BERYLLIUM TRIFLUORIDE ION (BEFb)
2c: BERYLLIUM TRIFLUORIDE ION (BEFc)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
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Label:
No.
Name
Count
Type
Full Name
1
ADP
6
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
BEF
6
Ligand/Ion
BERYLLIUM TRIFLUORIDE ION
3
MG
-1
Ligand/Ion
MAGNESIUM ION
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Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
BEF A:157 , ADP A:158 , HOH A:619 , HOH A:626 , HOH A:693
BINDING SITE FOR RESIDUE MG A 156
2
AC2
SOFTWARE
BEF B:157 , ADP B:158 , HOH B:620 , HOH B:706 , HOH B:779
BINDING SITE FOR RESIDUE MG B 156
3
AC3
SOFTWARE
BEF C:157 , ADP C:158 , HOH C:643 , HOH C:777 , HOH C:778
BINDING SITE FOR RESIDUE MG C 156
4
AC4
SOFTWARE
LYS A:16 , TYR A:56 , ARG A:92 , ARG A:109 , HIS A:122 , GLY A:123 , MG A:156 , ADP A:158 , HOH A:619 , HOH A:626
BINDING SITE FOR RESIDUE BEF A 157
5
AC5
SOFTWARE
LYS A:16 , HIS A:59 , PHE A:64 , LEU A:68 , ARG A:92 , THR A:98 , ARG A:109 , VAL A:116 , ASN A:119 , MG A:156 , BEF A:157 , HOH A:619 , HOH A:626 , HOH A:681 , HOH A:693 , HOH A:729
BINDING SITE FOR RESIDUE ADP A 158
6
AC6
SOFTWARE
LYS B:16 , TYR B:56 , ARG B:92 , ARG B:109 , HIS B:122 , GLY B:123 , MG B:156 , ADP B:158 , HOH B:620 , HOH B:779
BINDING SITE FOR RESIDUE BEF B 157
7
AC7
SOFTWARE
LYS A:60 , LYS B:16 , HIS B:59 , PHE B:64 , LEU B:68 , ARG B:92 , THR B:98 , ARG B:109 , VAL B:116 , ASN B:119 , MG B:156 , BEF B:157 , HOH B:706 , HOH B:779 , HOH B:802
BINDING SITE FOR RESIDUE ADP B 158
8
AC8
SOFTWARE
LYS C:16 , TYR C:56 , ARG C:109 , HIS C:122 , GLY C:123 , MG C:156 , ADP C:158 , HOH C:643 , HOH C:777
BINDING SITE FOR RESIDUE BEF C 157
9
AC9
SOFTWARE
LYS C:16 , TYR C:56 , HIS C:59 , PHE C:64 , LEU C:68 , ARG C:92 , THR C:98 , ARG C:109 , VAL C:116 , ASN C:119 , MG C:156 , BEF C:157 , HOH C:617 , HOH C:643 , HOH C:778
BINDING SITE FOR RESIDUE ADP C 158
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(1, 6)
Info
All PROSITE Patterns/Profiles
1: NDP_KINASES (A:119-127,B:119-127,C:119-127)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
NDP_KINASES
PS00469
Nucleoside diphosphate kinases active site.
NDKC_DICDI
119-127
6
A:119-127
B:119-127
C:119-127
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
(1, 3)
Info
All SCOP Domains
1a: SCOP_d2befa_ (A:)
1b: SCOP_d2befb_ (B:)
1c: SCOP_d2befc_ (C:)
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Protein Domains
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Organisms
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(
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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)
Slime mold (Dictyostelium discoideum) [TaxId: 44689]
(21)
1a
d2befa_
A:
1b
d2befb_
B:
1c
d2befc_
C:
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CATH Domains
(1, 3)
Info
all CATH domains
1a: CATH_2befA00 (A:6-155)
1b: CATH_2befB00 (B:6-155)
1c: CATH_2befC00 (C:6-155)
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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)
Dictyostelium discoideum. Organism_taxid: 44689.
(15)
1a
2befA00
A:6-155
1b
2befB00
B:6-155
1c
2befC00
C:6-155
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Pfam Domains
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