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3BBF
Asym. Unit
Info
Asym.Unit (174 KB)
Biol.Unit 1 (167 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE NM23-H2 TRANSCRIPTION FACTOR COMPLEX WITH GDP
Authors
:
A. Weichsel, W. R. Montfort
Date
:
09 Nov 07 (Deposition) - 23 Sep 08 (Release) - 04 Aug 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Transcription Factor, Cancer, Kinase, Nm23 Gen, Hexamer, Activator, Anti-Oncogene, Atp-Binding, Cell Cycle, Dna-Binding, Magnesium, Metal-Binding, Nucleotide Metabolism, Nucleotide-Binding, Nucleus, Phosphorylation, Transcription Regulation, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. S. Dexheimer, S. S. Carey, S. Zuohe, V. M. Gokhale, X. Hu, L. B. Murata E. M. Maes, A. Weichsel, D. Sun, E. J. Meuillet, W. R. Montfort, L. H. Hurley
Nm23-H2 May Play An Indirect Role In Transcriptional Activation Of C-Myc Gene Expression But Does Not Cleave The Nuclease Hypersensitive Element Iii1.
Mol. Cancer Ther. V. 8 1363 2009
(for further references see the
PDB file header
)
[
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]
Hetero Components
(3, 14)
Info
All Hetero Components
1a: 2,3-DIHYDROXY-1,4-DITHIOBUTANE (DTTa)
1b: 2,3-DIHYDROXY-1,4-DITHIOBUTANE (DTTb)
2a: GUANOSINE-5'-DIPHOSPHATE (GDPa)
2b: GUANOSINE-5'-DIPHOSPHATE (GDPb)
2c: GUANOSINE-5'-DIPHOSPHATE (GDPc)
2d: GUANOSINE-5'-DIPHOSPHATE (GDPd)
2e: GUANOSINE-5'-DIPHOSPHATE (GDPe)
2f: GUANOSINE-5'-DIPHOSPHATE (GDPf)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DTT
2
Ligand/Ion
2,3-DIHYDROXY-1,4-DITHIOBUTANE
2
GDP
6
Ligand/Ion
GUANOSINE-5'-DIPHOSPHATE
3
MG
6
Ligand/Ion
MAGNESIUM ION
[
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Sites
(14, 14)
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)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GDP A:160 , HOH A:166 , HOH A:171 , HOH A:215 , HOH A:220 , HOH A:225
BINDING SITE FOR RESIDUE MG A 161
02
AC2
SOFTWARE
GDP B:160 , HOH B:174 , HOH B:201 , HOH B:220 , HOH B:282 , HOH B:293
BINDING SITE FOR RESIDUE MG B 161
03
AC3
SOFTWARE
GDP C:160 , HOH C:170 , HOH C:191 , HOH C:211 , HOH C:214 , HOH C:249
BINDING SITE FOR RESIDUE MG C 161
04
AC4
SOFTWARE
GDP D:160 , HOH D:193 , HOH D:221 , HOH D:227 , HOH D:235 , HOH D:257
BINDING SITE FOR RESIDUE MG D 161
05
AC5
SOFTWARE
GDP E:160 , HOH E:173 , HOH E:219 , HOH E:223
BINDING SITE FOR RESIDUE MG E 161
06
AC6
SOFTWARE
ASP F:54 , GDP F:160 , HOH F:200 , HOH F:235 , HOH F:242
BINDING SITE FOR RESIDUE MG F 161
07
AC7
SOFTWARE
LYS A:12 , TYR A:52 , LEU A:55 , PHE A:60 , LEU A:64 , ARG A:88 , THR A:94 , VAL A:112 , GLY A:113 , ASN A:115 , MG A:161 , HOH A:166 , HOH A:168 , HOH A:171 , HOH A:197 , HOH A:224 , HOH A:225 , HOH A:232 , HOH A:250 , HOH A:259 , HOH A:298 , GLU B:152 , HOH B:170
BINDING SITE FOR RESIDUE GDP A 160
08
AC8
SOFTWARE
LYS B:12 , TYR B:52 , LEU B:55 , PHE B:60 , LEU B:64 , ARG B:88 , THR B:94 , VAL B:112 , GLY B:113 , ASN B:115 , MG B:161 , HOH B:175 , HOH B:190 , HOH B:201 , HOH B:220 , HOH B:221 , HOH B:282 , GLU C:152
BINDING SITE FOR RESIDUE GDP B 160
09
AC9
SOFTWARE
GLU A:152 , ALA B:2 , ASN B:3 , LYS C:12 , TYR C:52 , LEU C:55 , PHE C:60 , LEU C:64 , ARG C:88 , THR C:94 , VAL C:112 , GLY C:113 , ASN C:115 , MG C:161 , HOH C:172 , HOH C:185 , HOH C:191 , HOH C:194 , HOH C:198 , HOH C:211 , HOH C:214 , HOH C:258
BINDING SITE FOR RESIDUE GDP C 160
10
BC1
SOFTWARE
LYS D:12 , TYR D:52 , LEU D:55 , PHE D:60 , LEU D:64 , ARG D:88 , THR D:94 , VAL D:112 , GLY D:113 , ASN D:115 , MG D:161 , HOH D:169 , HOH D:174 , HOH D:202 , HOH D:221 , HOH D:229 , HOH D:234 , HOH D:235 , HOH D:257 , GLU F:152
BINDING SITE FOR RESIDUE GDP D 160
11
BC2
SOFTWARE
GLU D:152 , LYS E:12 , TYR E:52 , LEU E:55 , PHE E:60 , LEU E:64 , ARG E:88 , THR E:94 , VAL E:112 , ASN E:115 , MG E:161 , HOH E:169 , HOH E:173 , HOH E:215 , HOH E:217 , HOH E:223 , HOH E:228
BINDING SITE FOR RESIDUE GDP E 160
12
BC3
SOFTWARE
GLU E:152 , LYS F:12 , TYR F:52 , LEU F:55 , PHE F:60 , LEU F:64 , ARG F:88 , THR F:94 , VAL F:112 , ASN F:115 , MG F:161 , HOH F:170 , HOH F:184 , HOH F:193 , HOH F:227 , HOH F:235 , HOH F:242
BINDING SITE FOR RESIDUE GDP F 160
13
BC4
SOFTWARE
GLN A:17 , ARG A:18 , GLY A:19 , CYS B:145 , ALA B:146 , HOH B:199 , HOH B:212 , HOH B:225 , HOH B:226 , CYS D:145 , ALA D:146 , HOH D:215 , GLN E:17 , ARG E:18 , GLY E:19
BINDING SITE FOR RESIDUE DTT B 162
14
BC5
SOFTWARE
GLN B:17 , ARG B:18 , GLY B:19 , CYS C:145 , ALA C:146 , HOH C:226 , HOH C:241 , GLU E:29 , CYS E:145 , ALA E:146 , HOH E:164 , GLN F:17 , ARG F:18 , GLY F:19 , HOH F:230
BINDING SITE FOR RESIDUE DTT F 162
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 6)
Info
All PROSITE Patterns/Profiles
1: NDP_KINASES (A:115-123,B:115-123,C:115-123,D:11...)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
NDP_KINASES
PS00469
Nucleoside diphosphate kinases active site.
NDKB_HUMAN
115-123
6
A:115-123
B:115-123
C:115-123
D:115-123
E:115-123
F:115-123
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Exons
(0, 0)
Info
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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, 6)
Info
All SCOP Domains
1a: SCOP_d3bbfa_ (A:)
1b: SCOP_d3bbfb_ (B:)
1c: SCOP_d3bbfc_ (C:)
1d: SCOP_d3bbfd_ (D:)
1e: SCOP_d3bbfe_ (E:)
1f: SCOP_d3bbff_ (F:)
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Protein Domains
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(
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Organisms
(
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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)
Human (Homo sapiens) [TaxId: 9606]
(5)
1a
d3bbfa_
A:
1b
d3bbfb_
B:
1c
d3bbfc_
C:
1d
d3bbfd_
D:
1e
d3bbfe_
E:
1f
d3bbff_
F:
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CATH Domains
(0, 0)
Info
all CATH domains
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Pfam Domains
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Chain D
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Chain F
Asymmetric Unit 1
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Asym.Unit (174 KB)
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