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2VD3
Biol. Unit 1
Info
Asym.Unit (99 KB)
Biol.Unit 1 (272 KB)
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(1)
Title
:
THE STRUCTURE OF HISTIDINE INHIBITED HISG FROM METHANOBACTERIUM THERMOAUTOTROPHICUM
Authors
:
B. Lohkamp, T. Schweikert, A. J. Lapthorn
Date
:
28 Sep 07 (Deposition) - 04 Nov 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.45
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (3x)
Keywords
:
Metal-Binding, Glycosyltransferase, Hisg, Histidine, Magnesium, Transferase, Histidine Biosynthesis, Amino-Acid Biosynthesis, Atp Phosphoribosyl Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. Lohkamp, T. Schweikert, A. J. Lapthorn
The Structure Of Histidine Inhibited Hisg From Methanobacterium Thermoautotrophicum
To Be Published
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close entry info
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Hetero Components
(4, 33)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
1e: CHLORIDE ION (CLe)
1f: CHLORIDE ION (CLf)
1g: CHLORIDE ION (CLg)
1h: CHLORIDE ION (CLh)
1i: CHLORIDE ION (CLi)
2a: HISTIDINE (HISa)
2b: HISTIDINE (HISb)
3a: IMIDAZOLE (IMDa)
3b: IMIDAZOLE (IMDb)
3c: IMIDAZOLE (IMDc)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
4d: MAGNESIUM ION (MGd)
4e: MAGNESIUM ION (MGe)
4f: MAGNESIUM ION (MGf)
4g: MAGNESIUM ION (MGg)
4h: MAGNESIUM ION (MGh)
4i: MAGNESIUM ION (MGi)
5a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
5b: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDb)
5c: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDc)
5d: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDd)
5e: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDe)
6a: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
-1
Ligand/Ion
CHLORIDE ION
2
HIS
6
Mod. Amino Acid
HISTIDINE
3
IMD
9
Ligand/Ion
IMIDAZOLE
4
MG
-1
Ligand/Ion
MAGNESIUM ION
5
MPD
15
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
6
MRD
3
Ligand/Ion
(4R)-2-METHYLPENTANE-2,4-DIOL
[
close Hetero Component info
]
Sites
(28, 28)
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)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:160
BINDING SITE FOR RESIDUE CL A1007
02
AC2
SOFTWARE
GLU A:125 , ASP A:134 , ALA A:135
BINDING SITE FOR RESIDUE IMD A1288
03
AC3
SOFTWARE
LYS A:260 , HOH A:2009
BINDING SITE FOR RESIDUE IMD A1289
04
AC4
SOFTWARE
MET A:218 , LEU A:219 , ASN A:220 , GLY A:235 , MET A:236 , THR A:237 , GLY A:238 , THR A:240 , VAL A:256 , ASP A:276
BINDING SITE FOR RESIDUE HIS A1290
05
AC5
SOFTWARE
PRO A:1 , LYS A:194 , GLY A:196 , ILE A:197
BINDING SITE FOR RESIDUE CL A1291
06
AC6
SOFTWARE
LYS A:183
BINDING SITE FOR RESIDUE CL A1292
07
AC7
SOFTWARE
GLU A:119 , THR A:157
BINDING SITE FOR RESIDUE CL A1293
08
AC8
SOFTWARE
ASP A:158 , LEU A:159
BINDING SITE FOR RESIDUE MG A1294
09
AC9
SOFTWARE
GLU A:82
BINDING SITE FOR RESIDUE MG A1295
10
BC1
SOFTWARE
GLU A:22 , GLY A:27 , GLN A:41
BINDING SITE FOR RESIDUE MG A1296
11
BC2
SOFTWARE
ASP A:175
BINDING SITE FOR RESIDUE MG A1297
12
BC3
SOFTWARE
GLU A:119 , GLU A:139 , LEU A:140 , THR A:141
BINDING SITE FOR RESIDUE MPD A1298
13
BC4
SOFTWARE
GLY A:151 , VAL A:152 , ASP A:154
BINDING SITE FOR RESIDUE MRD A1299
14
BC5
SOFTWARE
ARG A:4 , GLU A:46 , ALA A:63 , ASP A:65 , LYS A:194
BINDING SITE FOR RESIDUE MPD A1300
15
BC6
SOFTWARE
ASP A:61 , GLU B:136
BINDING SITE FOR RESIDUE MG B1118
16
BC7
SOFTWARE
LYS B:88 , ASP B:109 , ASP B:258
BINDING SITE FOR RESIDUE IMD B1288
17
BC8
SOFTWARE
GLU B:119 , THR B:157
BINDING SITE FOR RESIDUE CL B1289
18
BC9
SOFTWARE
PRO B:1 , GLY B:196 , ILE B:197
BINDING SITE FOR RESIDUE CL B1290
19
CC1
SOFTWARE
LEU B:171 , ARG B:172 , VAL B:173
BINDING SITE FOR RESIDUE CL B1291
20
CC2
SOFTWARE
ALA B:52 , ALA B:53
BINDING SITE FOR RESIDUE CL B1292
21
CC3
SOFTWARE
LYS B:10 , ARG B:51 , ALA B:52
BINDING SITE FOR RESIDUE MG B1293
22
CC4
SOFTWARE
GLU B:145 , ASP B:158
BINDING SITE FOR RESIDUE MG B1294
23
CC5
SOFTWARE
GLY B:11 , ARG B:12 , SER B:14 , GLU B:15
BINDING SITE FOR RESIDUE MG B1295
24
CC6
SOFTWARE
SER B:9 , HOH B:2001 , HOH B:2006
BINDING SITE FOR RESIDUE MG B1296
25
CC7
SOFTWARE
GLU B:119 , GLU B:139 , LEU B:140 , THR B:141
BINDING SITE FOR RESIDUE MPD B1297
26
CC8
SOFTWARE
LYS B:2 , ARG B:4 , ALA B:63 , ASP B:65
BINDING SITE FOR RESIDUE MPD B1298
27
CC9
SOFTWARE
SER B:93 , SER B:160 , SER B:161 , GLY B:163
BINDING SITE FOR RESIDUE MPD B1299
28
DC1
SOFTWARE
LEU B:219 , ASN B:220 , GLY B:235 , MET B:236 , THR B:237 , GLY B:238 , THR B:240 , ALA B:255 , VAL B:256 , ASP B:276 , HOH B:2022
BINDING SITE FOR RESIDUE HIS B1300
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 6)
Info
All PROSITE Patterns/Profiles
1: ATP_P_PHORIBOSYLTR (A:145-166,B:145-166)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ATP_P_PHORIBOSYLTR
PS01316
ATP phosphoribosyltransferase signature.
HIS1_METTH
145-166
6
A:145-166
B:145-166
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d2vd3a2 (A:213-287)
1b: SCOP_d2vd3b2 (B:213-287)
2a: SCOP_d2vd3a1 (A:-1-212)
2b: SCOP_d2vd3b1 (B:-1-212)
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Folds
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Superfamilies
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Families
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
GlnB-like
(79)
Family
:
automated matches
(20)
Protein domain
:
automated matches
(20)
Methanobacterium thermoautotrophicum [TaxId: 187420]
(1)
1a
d2vd3a2
A:213-287
1b
d2vd3b2
B:213-287
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Periplasmic binding protein-like II
(813)
Superfamily
:
Periplasmic binding protein-like II
(813)
Family
:
automated matches
(267)
Protein domain
:
automated matches
(267)
Methanobacterium thermoautotrophicum [TaxId: 187420]
(1)
2a
d2vd3a1
A:-1-212
2b
d2vd3b1
B:-1-212
[
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_2vd3A03 (A:214-287)
1b: CATH_2vd3B03 (B:214-287)
2a: CATH_2vd3A02 (A:90-180)
2b: CATH_2vd3B02 (B:90-180)
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Homologous Superfamilies
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.120, no name defined]
(37)
Methanobacterium thermoautotrophicum. Organism_taxid: 187420. Strain:deltah.
(1)
1a
2vd3A03
A:214-287
1b
2vd3B03
B:214-287
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
D-Maltodextrin-Binding Protein; domain 2
(600)
Homologous Superfamily
:
Periplasmic binding protein-like II
(486)
Methanobacterium thermoautotrophicum. Organism_taxid: 187420. Strain:deltah.
(1)
2a
2vd3A02
A:90-180
2b
2vd3B02
B:90-180
[
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_HisG_C_2vd3B01 (B:210-285)
1b: PFAM_HisG_C_2vd3B02 (B:210-285)
2a: PFAM_HisG_2vd3B03 (B:50-209)
2b: PFAM_HisG_2vd3B04 (B:50-209)
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Clans
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Organisms
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)
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)
Clan
:
GlnB-like
(50)
Family
:
HisG_C
(3)
Methanobacterium thermoautotrophicum (strain Delta H)
(1)
1a
HisG_C-2vd3B01
B:210-285
1b
HisG_C-2vd3B02
B:210-285
Clan
:
PBP
(391)
Family
:
HisG
(10)
Methanobacterium thermoautotrophicum (strain Delta H)
(1)
2a
HisG-2vd3B03
B:50-209
2b
HisG-2vd3B04
B:50-209
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