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Asym. Unit
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Asym.Unit (494 KB)
Biol.Unit 1 (483 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF BOVINE GLUTAMATE DEHYDROGENASE COMPLEXED WITH HEXACHLOROPHENE
Authors
:
M. Li, T. J. Smith
Date
:
07 Oct 08 (Deposition) - 09 Jun 09 (Release) - 01 Sep 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Glutamate Dehydrogenase, Hexachlorophene, Inhibitor, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Li, C. J. Smith, M. T. Walker, T. J. Smith
Novel Inhibitors Complexed With Glutamate Dehydrogenase: Allosteric Regulation By Control Of Protein Dynamics
J. Biol. Chem. V. 284 22988 2009
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 24)
Info
All Hetero Components
1a: GLUTAMIC ACID (GLUa)
1b: GLUTAMIC ACID (GLUb)
1c: GLUTAMIC ACID (GLUc)
1d: GLUTAMIC ACID (GLUd)
1e: GLUTAMIC ACID (GLUe)
1f: GLUTAMIC ACID (GLUf)
2a: GUANOSINE-5'-TRIPHOSPHATE (GTPa)
2b: GUANOSINE-5'-TRIPHOSPHATE (GTPb)
2c: GUANOSINE-5'-TRIPHOSPHATE (GTPc)
2d: GUANOSINE-5'-TRIPHOSPHATE (GTPd)
2e: GUANOSINE-5'-TRIPHOSPHATE (GTPe)
2f: GUANOSINE-5'-TRIPHOSPHATE (GTPf)
3a: 2,2'-METHANEDIYLBIS(3,4,6-TRICHLOR... (H3Pa)
3b: 2,2'-METHANEDIYLBIS(3,4,6-TRICHLOR... (H3Pb)
3c: 2,2'-METHANEDIYLBIS(3,4,6-TRICHLOR... (H3Pc)
3d: 2,2'-METHANEDIYLBIS(3,4,6-TRICHLOR... (H3Pd)
3e: 2,2'-METHANEDIYLBIS(3,4,6-TRICHLOR... (H3Pe)
3f: 2,2'-METHANEDIYLBIS(3,4,6-TRICHLOR... (H3Pf)
4a: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPa)
4b: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPb)
4c: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPc)
4d: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPd)
4e: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPe)
4f: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GLU
6
Mod. Amino Acid
GLUTAMIC ACID
2
GTP
6
Ligand/Ion
GUANOSINE-5'-TRIPHOSPHATE
3
H3P
6
Ligand/Ion
2,2'-METHANEDIYLBIS(3,4,6-TRICHLOROPHENOL)
4
NDP
6
Ligand/Ion
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
[
close Hetero Component info
]
Sites
(18, 18)
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)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:94 , LYS A:134 , ASP A:168 , MET A:169 , SER A:170 , ARG A:211 , THR A:215 , PHE A:252 , GLY A:253 , ASN A:254 , VAL A:255 , GLU A:275 , SER A:276 , ALA A:326 , SER A:327 , GLN A:330 , ALA A:348 , ASN A:349 , ASN A:374 , GLU A:550
BINDING SITE FOR RESIDUE NDP A 551
02
AC2
SOFTWARE
ILE A:212 , SER A:213 , ARG A:217 , LEU A:257 , HIS A:258 , ARG A:261 , TYR A:262 , GLU A:292 , LYS A:446 , HIS A:450
BINDING SITE FOR RESIDUE GTP A 553
03
AC3
SOFTWARE
ARG B:94 , LYS B:134 , PRO B:167 , ASP B:168 , MET B:169 , SER B:170 , ARG B:211 , THR B:215 , GLN B:250 , PHE B:252 , GLY B:253 , ASN B:254 , VAL B:255 , GLU B:275 , SER B:276 , ALA B:326 , SER B:327 , GLN B:330 , GLY B:347 , ALA B:348 , ASN B:349 , ASN B:374 , GLU B:550
BINDING SITE FOR RESIDUE NDP B 551
04
AC4
SOFTWARE
HIS B:209 , ARG B:217 , HIS B:258 , ARG B:261 , TYR B:262 , ARG B:265 , GLU B:292 , HIS B:450 , HOH B:554
BINDING SITE FOR RESIDUE GTP B 553
05
AC5
SOFTWARE
ARG C:94 , LYS C:134 , PRO C:167 , ASP C:168 , MET C:169 , SER C:170 , ARG C:211 , THR C:215 , PHE C:252 , GLY C:253 , ASN C:254 , VAL C:255 , GLU C:275 , SER C:276 , ALA C:325 , ALA C:326 , GLN C:330 , GLY C:347 , ASN C:349 , ASN C:374 , GLU C:550 , HOH C:582 , HOH C:590
BINDING SITE FOR RESIDUE NDP C 551
06
AC6
SOFTWARE
HIS C:209 , ARG C:217 , HIS C:258 , ARG C:261 , TYR C:262 , ARG C:265 , LYS C:289 , GLU C:292
BINDING SITE FOR RESIDUE GTP C 553
07
AC7
SOFTWARE
ARG D:94 , LYS D:134 , ASP D:168 , MET D:169 , SER D:170 , ARG D:211 , THR D:215 , GLY D:251 , PHE D:252 , GLY D:253 , ASN D:254 , VAL D:255 , GLU D:275 , SER D:276 , ALA D:325 , ALA D:326 , SER D:327 , GLN D:330 , GLY D:347 , ALA D:348 , ASN D:349 , ASN D:374 , GLU D:550 , HOH D:560
BINDING SITE FOR RESIDUE NDP D 551
08
AC8
SOFTWARE
HIS D:209 , ARG D:217 , HIS D:258 , ARG D:261 , TYR D:262 , ARG D:265 , GLU D:292 , HIS D:450 , HOH D:554 , HOH D:567 , HOH D:573 , HOH D:586
BINDING SITE FOR RESIDUE GTP D 553
09
AC9
SOFTWARE
ARG E:94 , LYS E:134 , ASP E:168 , MET E:169 , SER E:170 , ARG E:211 , THR E:215 , GLN E:250 , PHE E:252 , GLY E:253 , ASN E:254 , VAL E:255 , GLU E:275 , SER E:276 , ALA E:325 , ALA E:326 , SER E:327 , GLN E:330 , ALA E:348 , ASN E:349 , GLU E:550
BINDING SITE FOR RESIDUE NDP E 551
10
BC1
SOFTWARE
HIS E:209 , ARG E:217 , LEU E:257 , HIS E:258 , ARG E:261 , TYR E:262 , ARG E:265 , GLU E:292 , HIS E:450 , HOH E:572
BINDING SITE FOR RESIDUE GTP E 553
11
BC2
SOFTWARE
ARG F:94 , LYS F:134 , ASP F:168 , MET F:169 , ARG F:211 , THR F:215 , PHE F:252 , GLY F:253 , ASN F:254 , VAL F:255 , GLU F:275 , SER F:276 , ALA F:326 , SER F:327 , GLN F:330 , GLY F:347 , ALA F:348 , ASN F:349 , ASN F:374
BINDING SITE FOR RESIDUE NDP F 551
12
BC3
SOFTWARE
HIS F:209 , ARG F:217 , HIS F:258 , ARG F:261 , TYR F:262 , ARG F:265 , GLU F:292 , HIS F:450
BINDING SITE FOR RESIDUE GTP F 553
13
BC4
SOFTWARE
TYR A:190 , H3P A:552 , ALA B:153 , ILE B:158 , TYR B:183 , LYS E:154
BINDING SITE FOR RESIDUE H3P B 552
14
BC5
SOFTWARE
THR A:186 , ILE A:187 , TYR A:190 , HOH A:560 , H3P B:552 , MET E:150 , THR E:186 , ILE E:187 , HIS E:189
BINDING SITE FOR RESIDUE H3P A 552
15
BC6
SOFTWARE
ALA A:153 , ALA D:153 , LYS D:154 , TYR E:190 , H3P F:552
BINDING SITE FOR RESIDUE H3P D 552
16
BC7
SOFTWARE
MET D:150 , THR D:186 , ILE D:187 , HIS D:189 , H3P D:552 , LYS F:154 , THR F:186 , ILE F:187 , TYR F:190
BINDING SITE FOR RESIDUE H3P F 552
17
BC8
SOFTWARE
ALA C:153 , LYS C:154 , H3P C:554 , TYR D:190 , ALA F:153 , LYS F:154 , HOH F:572
BINDING SITE FOR RESIDUE H3P C 552
18
BC9
SOFTWARE
THR B:186 , ILE B:187 , TYR B:190 , MET C:150 , THR C:186 , ILE C:187 , HIS C:189 , H3P C:552 , HOH C:574
BINDING SITE FOR RESIDUE H3P C 554
[
close Site info
]
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: GLFV_DEHYDROGENASE (A:120-133,B:120-133,C:120-133,D:12...)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GLFV_DEHYDROGENASE
PS00074
Glu / Leu / Phe / Val dehydrogenases active site.
DHE3_BOVIN
177-190
6
A:120-133
B:120-133
C:120-133
D:120-133
E:120-133
F:120-133
[
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Exons
(0, 0)
Info
All Exons
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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
(2, 12)
Info
All SCOP Domains
1a: SCOP_d3etea1 (A:4-208)
1b: SCOP_d3eteb1 (B:4-208)
1c: SCOP_d3etec1 (C:4-208)
1d: SCOP_d3eted1 (D:4-208)
1e: SCOP_d3etee1 (E:4-208)
1f: SCOP_d3etef1 (F:4-208)
2a: SCOP_d3etea2 (A:209-498)
2b: SCOP_d3eteb2 (B:209-498)
2c: SCOP_d3etec2 (C:209-498)
2d: SCOP_d3eted2 (D:209-498)
2e: SCOP_d3etee2 (E:209-498)
2f: SCOP_d3etef2 (F:209-498)
View:
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(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Aminoacid dehydrogenase-like, N-terminal domain
(100)
Superfamily
:
Aminoacid dehydrogenase-like, N-terminal domain
(100)
Family
:
Aminoacid dehydrogenases
(28)
Protein domain
:
automated matches
(4)
Cow (Bos taurus) [TaxId: 9913]
(3)
1a
d3etea1
A:4-208
1b
d3eteb1
B:4-208
1c
d3etec1
C:4-208
1d
d3eted1
D:4-208
1e
d3etee1
E:4-208
1f
d3etef1
F:4-208
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Aminoacid dehydrogenase-like, C-terminal domain
(67)
Protein domain
:
automated matches
(5)
Cow (Bos taurus) [TaxId: 9913]
(3)
2a
d3etea2
A:209-498
2b
d3eteb2
B:209-498
2c
d3etec2
C:209-498
2d
d3eted2
D:209-498
2e
d3etee2
E:209-498
2f
d3etef2
F:209-498
[
close SCOP info
]
CATH Domains
(3, 18)
Info
all CATH domains
1a: CATH_3eteA02 (A:57-205)
1b: CATH_3eteE02 (E:57-205)
1c: CATH_3eteF02 (F:57-205)
1d: CATH_3eteB02 (B:57-205)
1e: CATH_3eteC02 (C:57-205)
1f: CATH_3eteD02 (D:57-205)
2a: CATH_3eteA03 (A:206-498)
2b: CATH_3eteD03 (D:206-498)
2c: CATH_3eteE03 (E:206-498)
2d: CATH_3eteF03 (F:206-498)
2e: CATH_3eteB03 (B:206-498)
2f: CATH_3eteC03 (C:206-498)
3a: CATH_3eteA01 (A:4-56)
3b: CATH_3eteE01 (E:4-56)
3c: CATH_3eteF01 (F:4-56)
3d: CATH_3eteB01 (B:4-56)
3e: CATH_3eteC01 (C:4-56)
3f: CATH_3eteD01 (D:4-56)
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)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Leucine Dehydrogenase; Chain A, domain 1
(52)
Homologous Superfamily
:
Leucine Dehydrogenase, chain A, domain 1
(52)
Bos taurus. Organism_taxid: 9913.
(2)
1a
3eteA02
A:57-205
1b
3eteE02
E:57-205
1c
3eteF02
F:57-205
1d
3eteB02
B:57-205
1e
3eteC02
C:57-205
1f
3eteD02
D:57-205
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Bos taurus. Organism_taxid: 9913.
(3)
2a
3eteA03
A:206-498
2b
3eteD03
D:206-498
2c
3eteE03
E:206-498
2d
3eteF03
F:206-498
2e
3eteB03
B:206-498
2f
3eteC03
C:206-498
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Helix Hairpins
(718)
Homologous Superfamily
:
[code=1.10.287.140, no name defined]
(11)
Bos taurus. Organism_taxid: 9913.
(2)
3a
3eteA01
A:4-56
3b
3eteE01
E:4-56
3c
3eteF01
F:4-56
3d
3eteB01
B:4-56
3e
3eteC01
C:4-56
3f
3eteD01
D:4-56
[
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]
Pfam Domains
(0, 0)
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all PFAM domains
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