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2BVC
Asym. Unit
Info
Asym.Unit (475 KB)
Biol.Unit 1 (922 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS GLUTAMINE SYNTHETASE IN COMPLEX WITH A TRANSITION STATE MIMIC
Authors
:
W. W. Krajewski, T. A. Jones, S. L. Mowbray
Date
:
23 Jun 05 (Deposition) - 07 Jul 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (2x)
Keywords
:
Ligase, Transition State Mimic, Synthetase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
W. W. Krajewski, T. A. Jones, S. L. Mowbray
Structure Of Mycobacterium Tuberculosis Glutamine Synthetase In Complex With A Transition-State Mimic Provides Functional Insights.
Proc. Natl. Acad. Sci. Usa V. 102 10499 2005
[
close entry info
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Hetero Components
(4, 36)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
1b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
1c: ADENOSINE-5'-DIPHOSPHATE (ADPc)
1d: ADENOSINE-5'-DIPHOSPHATE (ADPd)
1e: ADENOSINE-5'-DIPHOSPHATE (ADPe)
1f: ADENOSINE-5'-DIPHOSPHATE (ADPf)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
2f: CHLORIDE ION (CLf)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
3g: MAGNESIUM ION (MGg)
3h: MAGNESIUM ION (MGh)
3i: MAGNESIUM ION (MGi)
3j: MAGNESIUM ION (MGj)
3k: MAGNESIUM ION (MGk)
3l: MAGNESIUM ION (MGl)
3m: MAGNESIUM ION (MGm)
3n: MAGNESIUM ION (MGn)
3o: MAGNESIUM ION (MGo)
3p: MAGNESIUM ION (MGp)
3q: MAGNESIUM ION (MGq)
3r: MAGNESIUM ION (MGr)
4a: L-METHIONINE-S-SULFOXIMINE PHOSPHA... (P3Sa)
4b: L-METHIONINE-S-SULFOXIMINE PHOSPHA... (P3Sb)
4c: L-METHIONINE-S-SULFOXIMINE PHOSPHA... (P3Sc)
4d: L-METHIONINE-S-SULFOXIMINE PHOSPHA... (P3Sd)
4e: L-METHIONINE-S-SULFOXIMINE PHOSPHA... (P3Se)
4f: L-METHIONINE-S-SULFOXIMINE PHOSPHA... (P3Sf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
6
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
CL
6
Ligand/Ion
CHLORIDE ION
3
MG
18
Ligand/Ion
MAGNESIUM ION
4
P3S
6
Ligand/Ion
L-METHIONINE-S-SULFOXIMINE PHOSPHATE
[
close Hetero Component info
]
Sites
(36, 36)
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)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:135 , GLU A:219 , GLU A:227 , P3S A:500 , HOH A:2028
BINDING SITE FOR RESIDUE MG A 502
02
AC2
SOFTWARE
GLU A:133 , HIS A:276 , GLU A:366 , P3S A:500 , ADP A:501
BINDING SITE FOR RESIDUE MG A 503
03
AC3
SOFTWARE
GLU A:133 , GLU A:227 , P3S A:500 , ADP A:501 , HOH A:2067
BINDING SITE FOR RESIDUE MG A 504
04
AC4
SOFTWARE
SER F:424
BINDING SITE FOR RESIDUE CL A 505
05
AC5
SOFTWARE
GLU B:135 , GLU B:219 , GLU B:227 , P3S B:500 , HOH B:2091
BINDING SITE FOR RESIDUE MG B 502
06
AC6
SOFTWARE
GLU B:133 , HIS B:276 , GLU B:366 , ARG B:368 , P3S B:500 , ADP B:501
BINDING SITE FOR RESIDUE MG B 503
07
AC7
SOFTWARE
GLU B:133 , GLU B:227 , P3S B:500 , ADP B:501 , HOH B:2057
BINDING SITE FOR RESIDUE MG B 504
08
AC8
SOFTWARE
SER E:424
BINDING SITE FOR RESIDUE CL B 505
09
AC9
SOFTWARE
GLU C:135 , GLU C:219 , GLU C:227 , P3S C:500 , HOH C:2087
BINDING SITE FOR RESIDUE MG C 502
10
BC1
SOFTWARE
GLU C:133 , HIS C:276 , GLU C:366 , ARG C:368 , P3S C:500 , ADP C:501
BINDING SITE FOR RESIDUE MG C 503
11
BC2
SOFTWARE
GLU C:133 , GLU C:227 , P3S C:500 , ADP C:501 , HOH C:2053
BINDING SITE FOR RESIDUE MG C 504
12
BC3
SOFTWARE
SER A:424 , HOH A:2109
BINDING SITE FOR RESIDUE CL C 505
13
BC4
SOFTWARE
GLU D:135 , GLU D:219 , GLU D:227 , P3S D:500 , HOH D:2063
BINDING SITE FOR RESIDUE MG D 502
14
BC5
SOFTWARE
GLU D:133 , HIS D:276 , GLU D:366 , ARG D:368 , P3S D:500 , ADP D:501
BINDING SITE FOR RESIDUE MG D 503
15
BC6
SOFTWARE
GLU D:133 , GLU D:227 , P3S D:500 , ADP D:501 , HOH D:2059
BINDING SITE FOR RESIDUE MG D 504
16
BC7
SOFTWARE
SER B:424
BINDING SITE FOR RESIDUE CL D 505
17
BC8
SOFTWARE
GLU E:135 , GLU E:219 , GLU E:227 , P3S E:500 , MG E:504 , HOH E:2073
BINDING SITE FOR RESIDUE MG E 502
18
BC9
SOFTWARE
GLU E:133 , HIS E:276 , GLU E:366 , P3S E:500 , ADP E:501
BINDING SITE FOR RESIDUE MG E 503
19
CC1
SOFTWARE
GLU E:133 , GLU E:227 , P3S E:500 , ADP E:501 , MG E:502 , HOH E:2074
BINDING SITE FOR RESIDUE MG E 504
20
CC2
SOFTWARE
SER C:424
BINDING SITE FOR RESIDUE CL E 505
21
CC3
SOFTWARE
GLU F:135 , GLU F:219 , GLU F:227 , P3S F:500 , MG F:504 , HOH F:2027
BINDING SITE FOR RESIDUE MG F 502
22
CC4
SOFTWARE
GLU F:133 , HIS F:276 , GLU F:366 , P3S F:500 , ADP F:501
BINDING SITE FOR RESIDUE MG F 503
23
CC5
SOFTWARE
GLU F:133 , GLU F:227 , P3S F:500 , ADP F:501 , MG F:502 , HOH F:2105
BINDING SITE FOR RESIDUE MG F 504
24
CC6
SOFTWARE
SER D:424
BINDING SITE FOR RESIDUE CL F 505
25
CC7
SOFTWARE
GLU A:133 , GLU A:135 , GLU A:219 , GLU A:227 , GLY A:272 , HIS A:276 , ARG A:329 , TYR A:334 , GLU A:335 , ARG A:347 , GLU A:366 , ARG A:368 , ADP A:501 , MG A:502 , MG A:503 , MG A:504 , HOH A:2028 , HOH A:2047 , HOH A:2067 , HOH A:2116 , HOH A:2117 , ASP F:54
BINDING SITE FOR RESIDUE P3S A 500
26
CC8
SOFTWARE
GLU A:133 , GLU A:214 , LYS A:215 , GLU A:227 , ASN A:229 , TYR A:230 , GLN A:231 , PHE A:232 , HIS A:278 , SER A:280 , ARG A:347 , ARG A:352 , LYS A:361 , ARG A:364 , GLU A:366 , P3S A:500 , MG A:503 , MG A:504 , HOH A:2025 , HOH A:2067 , HOH A:2094 , HOH A:2118 , HOH A:2119
BINDING SITE FOR RESIDUE ADP A 501
27
CC9
SOFTWARE
ASP A:54 , GLU B:133 , GLU B:135 , GLU B:219 , GLU B:227 , GLY B:272 , HIS B:276 , ARG B:329 , GLU B:335 , ARG B:347 , GLU B:366 , ARG B:368 , ADP B:501 , MG B:502 , MG B:503 , MG B:504 , HOH B:2038 , HOH B:2076 , HOH B:2091 , HOH B:2092
BINDING SITE FOR RESIDUE P3S B 500
28
DC1
SOFTWARE
GLU B:133 , GLU B:214 , LYS B:215 , GLU B:227 , ASN B:229 , TYR B:230 , GLN B:231 , PHE B:232 , HIS B:278 , SER B:280 , ARG B:347 , ARG B:352 , LYS B:361 , ARG B:364 , GLU B:366 , P3S B:500 , MG B:503 , MG B:504 , HOH B:2014 , HOH B:2055 , HOH B:2057
BINDING SITE FOR RESIDUE ADP B 501
29
DC2
SOFTWARE
ASP B:54 , GLU C:133 , GLU C:135 , GLU C:219 , GLU C:227 , GLY C:272 , HIS C:276 , ARG C:329 , GLU C:335 , ARG C:347 , GLU C:366 , ARG C:368 , ADP C:501 , MG C:502 , MG C:503 , MG C:504 , HOH C:2038 , HOH C:2053 , HOH C:2069 , HOH C:2086 , HOH C:2087
BINDING SITE FOR RESIDUE P3S C 500
30
DC3
SOFTWARE
GLU C:133 , GLU C:214 , LYS C:215 , GLU C:227 , ASN C:229 , TYR C:230 , GLN C:231 , PHE C:232 , HIS C:278 , SER C:280 , ARG C:347 , ARG C:352 , LYS C:361 , ARG C:364 , GLU C:366 , P3S C:500 , MG C:503 , MG C:504 , HOH C:2015 , HOH C:2053
BINDING SITE FOR RESIDUE ADP C 501
31
DC4
SOFTWARE
ASP C:54 , GLU D:133 , GLU D:135 , GLU D:219 , GLU D:227 , GLY D:272 , HIS D:276 , ARG D:329 , GLU D:335 , ARG D:347 , GLU D:366 , ARG D:368 , ADP D:501 , MG D:502 , MG D:503 , MG D:504 , HOH D:2059 , HOH D:2061 , HOH D:2063 , HOH D:2078 , HOH D:2096
BINDING SITE FOR RESIDUE P3S D 500
32
DC5
SOFTWARE
GLU D:133 , GLU D:214 , LYS D:215 , GLU D:227 , ASN D:229 , TYR D:230 , GLN D:231 , PHE D:232 , HIS D:278 , SER D:280 , ARG D:347 , ARG D:352 , LYS D:361 , ARG D:364 , GLU D:366 , P3S D:500 , MG D:503 , MG D:504 , HOH D:2024 , HOH D:2058 , HOH D:2059
BINDING SITE FOR RESIDUE ADP D 501
33
DC6
SOFTWARE
ASP D:54 , GLU E:133 , GLU E:135 , GLU E:219 , GLU E:227 , GLY E:272 , GLY E:274 , HIS E:276 , ARG E:329 , GLU E:335 , ARG E:347 , GLU E:366 , ARG E:368 , ADP E:501 , MG E:502 , MG E:503 , MG E:504 , HOH E:2051 , HOH E:2072 , HOH E:2073 , HOH E:2074 , HOH E:2094
BINDING SITE FOR RESIDUE P3S E 500
34
DC7
SOFTWARE
GLY E:131 , GLU E:133 , GLU E:214 , LYS E:215 , GLU E:227 , ASN E:229 , TYR E:230 , GLN E:231 , PHE E:232 , HIS E:278 , SER E:280 , ARG E:347 , ARG E:352 , LYS E:361 , ARG E:364 , GLU E:366 , P3S E:500 , MG E:503 , MG E:504 , HOH E:2074 , HOH E:2101 , HOH E:2121
BINDING SITE FOR RESIDUE ADP E 501
35
DC8
SOFTWARE
ASP E:54 , GLU F:133 , GLU F:135 , GLU F:219 , GLU F:227 , GLY F:272 , HIS F:276 , ARG F:329 , GLU F:335 , ARG F:347 , GLU F:366 , ARG F:368 , ADP F:501 , MG F:502 , MG F:503 , MG F:504 , HOH F:2027 , HOH F:2065 , HOH F:2081 , HOH F:2105 , HOH F:2106
BINDING SITE FOR RESIDUE P3S F 500
36
DC9
SOFTWARE
GLU F:133 , GLU F:214 , LYS F:215 , GLU F:227 , ASN F:229 , TYR F:230 , GLN F:231 , PHE F:232 , HIS F:278 , SER F:280 , ARG F:347 , ARG F:352 , LYS F:361 , ARG F:364 , GLU F:366 , P3S F:500 , MG F:503 , MG F:504 , HOH F:2025 , HOH F:2105
BINDING SITE FOR RESIDUE ADP F 501
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 18)
Info
All PROSITE Patterns/Profiles
1: GLNA_1 (A:53-71,B:53-71,C:53-71,D:53-71,E:...)
2: GLNA_ATP (A:265-280,B:265-280,C:265-280,D:26...)
3: GLNA_ADENYLATION (A:394-406,B:394-406,C:394-406,D:39...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GLNA_1
PS00180
Glutamine synthetase signature 1.
GLN1B_MYCTO
53-71
6
A:53-71
B:53-71
C:53-71
D:53-71
E:53-71
F:53-71
GLN1B_MYCTU
53-71
6
A:53-71
B:53-71
C:53-71
D:53-71
E:53-71
F:53-71
2
GLNA_ATP
PS00181
Glutamine synthetase putative ATP-binding region signature.
GLN1B_MYCTO
265-280
6
A:265-280
B:265-280
C:265-280
D:265-280
E:265-280
F:265-280
GLN1B_MYCTU
265-280
6
A:265-280
B:265-280
C:265-280
D:265-280
E:265-280
F:265-280
3
GLNA_ADENYLATION
PS00182
Glutamine synthetase class-I adenylation site.
GLN1B_MYCTO
394-406
6
A:394-406
B:394-406
C:394-406
D:394-406
E:394-406
F:394-406
GLN1B_MYCTU
394-406
6
A:394-406
B:394-406
C:394-406
D:394-406
E:394-406
F:394-406
[
close PROSITE info
]
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_d2bvca1 (A:4-104)
1b: SCOP_d2bvce1 (E:4-104)
1c: SCOP_d2bvcf1 (F:4-104)
1d: SCOP_d2bvcb1 (B:4-104)
1e: SCOP_d2bvcc1 (C:4-104)
1f: SCOP_d2bvcd1 (D:4-104)
2a: SCOP_d2bvca2 (A:105-478)
2b: SCOP_d2bvce2 (E:105-478)
2c: SCOP_d2bvcf2 (F:105-478)
2d: SCOP_d2bvcb2 (B:105-478)
2e: SCOP_d2bvcc2 (C:105-478)
2f: SCOP_d2bvcd2 (D:105-478)
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Families
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Protein Domains
(
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(
)
Organisms
(
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(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
beta-Grasp (ubiquitin-like)
(1032)
Superfamily
:
Glutamine synthetase, N-terminal domain
(20)
Family
:
automated matches
(12)
Protein domain
:
automated matches
(12)
Mycobacterium tuberculosis [TaxId: 83332]
(6)
1a
d2bvca1
A:4-104
1b
d2bvce1
E:4-104
1c
d2bvcf1
F:4-104
1d
d2bvcb1
B:4-104
1e
d2bvcc1
C:4-104
1f
d2bvcd1
D:4-104
Fold
:
Glutamine synthetase/guanido kinase
(68)
Superfamily
:
Glutamine synthetase/guanido kinase
(68)
Family
:
automated matches
(18)
Protein domain
:
automated matches
(18)
Mycobacterium tuberculosis [TaxId: 83332]
(6)
2a
d2bvca2
A:105-478
2b
d2bvce2
E:105-478
2c
d2bvcf2
F:105-478
2d
d2bvcb2
B:105-478
2e
d2bvcc2
C:105-478
2f
d2bvcd2
D:105-478
[
close SCOP info
]
CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_2bvcA02 (A:108-466)
1b: CATH_2bvcB02 (B:108-466)
1c: CATH_2bvcC02 (C:108-466)
1d: CATH_2bvcD02 (D:108-466)
1e: CATH_2bvcE02 (E:108-466)
1f: CATH_2bvcF02 (F:108-466)
2a: CATH_2bvcA01 (A:5-107)
2b: CATH_2bvcB01 (B:5-107)
2c: CATH_2bvcC01 (C:5-107)
2d: CATH_2bvcD01 (D:5-107)
2e: CATH_2bvcE01 (E:5-107)
2f: CATH_2bvcF01 (F:5-107)
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Homologous Superfamilies
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Creatine Kinase; Chain A, domain 2
(27)
Homologous Superfamily
:
Creatine Kinase; Chain
(27)
Mycobacterium tuberculosis. Organism_taxid: 83332. Strain: h37rv.
(1)
1a
2bvcA02
A:108-466
1b
2bvcB02
B:108-466
1c
2bvcC02
C:108-466
1d
2bvcD02
D:108-466
1e
2bvcE02
E:108-466
1f
2bvcF02
F:108-466
Architecture
:
Roll
(3276)
Topology
:
Ubiquitin-like (UB roll)
(674)
Homologous Superfamily
:
[code=3.10.20.70, no name defined]
(11)
Mycobacterium tuberculosis. Organism_taxid: 83332. Strain: h37rv.
(1)
2a
2bvcA01
A:5-107
2b
2bvcB01
B:5-107
2c
2bvcC01
C:5-107
2d
2bvcD01
D:5-107
2e
2bvcE01
E:5-107
2f
2bvcF01
F:5-107
[
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Pfam Domains
(0, 0)
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all PFAM domains
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select residue range 5 to 10 in chain 'A'
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