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3GE1
Asym. Unit
Info
Asym.Unit (339 KB)
Biol.Unit 1 (324 KB)
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(1)
Title
:
2.7 ANGSTROM CRYSTAL STRUCTURE OF GLYCEROL KINASE (GLPK) FROM STAPHYLOCOCCUS AUREUS IN COMPLEX WITH ADP AND GLYCEROL
Authors
:
G. Minasov, J. Brunzelle, T. Skarina, O. Onopriyenko, S. N. Peterson, A. Savchenko, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
Date
:
24 Feb 09 (Deposition) - 24 Mar 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Glycerol Kinase, Glycerol, Adp, Idp00743, Atp-Binding, Glycerol Metabolism, Kinase, Nucleotide-Binding, Transferase, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. Minasov, J. Brunzelle, T. Skarina, O. Onopriyenko, S. N. Peterson, A. Savchenko, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
2. 7 Angstrom Crystal Structure Of Glycerol Kinase (Glpk) From Staphylococcus Aureus In Complex With Adp And Glycerol
To Be Published
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Hetero Components
(5, 63)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
1b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
1c: ADENOSINE-5'-DIPHOSPHATE (ADPc)
1d: ADENOSINE-5'-DIPHOSPHATE (ADPd)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
4a: SELENOMETHIONINE (MSEa)
4aa: SELENOMETHIONINE (MSEaa)
4ab: SELENOMETHIONINE (MSEab)
4ac: SELENOMETHIONINE (MSEac)
4ad: SELENOMETHIONINE (MSEad)
4ae: SELENOMETHIONINE (MSEae)
4af: SELENOMETHIONINE (MSEaf)
4ag: SELENOMETHIONINE (MSEag)
4ah: SELENOMETHIONINE (MSEah)
4ai: SELENOMETHIONINE (MSEai)
4aj: SELENOMETHIONINE (MSEaj)
4ak: SELENOMETHIONINE (MSEak)
4al: SELENOMETHIONINE (MSEal)
4am: SELENOMETHIONINE (MSEam)
4an: SELENOMETHIONINE (MSEan)
4ao: SELENOMETHIONINE (MSEao)
4ap: SELENOMETHIONINE (MSEap)
4aq: SELENOMETHIONINE (MSEaq)
4b: SELENOMETHIONINE (MSEb)
4c: SELENOMETHIONINE (MSEc)
4d: SELENOMETHIONINE (MSEd)
4e: SELENOMETHIONINE (MSEe)
4f: SELENOMETHIONINE (MSEf)
4g: SELENOMETHIONINE (MSEg)
4h: SELENOMETHIONINE (MSEh)
4i: SELENOMETHIONINE (MSEi)
4j: SELENOMETHIONINE (MSEj)
4k: SELENOMETHIONINE (MSEk)
4l: SELENOMETHIONINE (MSEl)
4m: SELENOMETHIONINE (MSEm)
4n: SELENOMETHIONINE (MSEn)
4o: SELENOMETHIONINE (MSEo)
4p: SELENOMETHIONINE (MSEp)
4q: SELENOMETHIONINE (MSEq)
4r: SELENOMETHIONINE (MSEr)
4s: SELENOMETHIONINE (MSEs)
4t: SELENOMETHIONINE (MSEt)
4u: SELENOMETHIONINE (MSEu)
4v: SELENOMETHIONINE (MSEv)
4w: SELENOMETHIONINE (MSEw)
4x: SELENOMETHIONINE (MSEx)
4y: SELENOMETHIONINE (MSEy)
4z: SELENOMETHIONINE (MSEz)
5a: PHOSPHATE ION (PO4a)
5b: PHOSPHATE ION (PO4b)
5c: PHOSPHATE ION (PO4c)
5d: PHOSPHATE ION (PO4d)
5e: PHOSPHATE ION (PO4e)
5f: PHOSPHATE ION (PO4f)
5g: PHOSPHATE ION (PO4g)
5h: PHOSPHATE ION (PO4h)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
4
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
CL
4
Ligand/Ion
CHLORIDE ION
3
GOL
4
Ligand/Ion
GLYCEROL
4
MSE
43
Mod. Amino Acid
SELENOMETHIONINE
5
PO4
8
Ligand/Ion
PHOSPHATE ION
[
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Sites
(20, 20)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:11 , THR A:12 , THR A:13 , ARG A:16 , GLY A:265 , THR A:266 , GLY A:309 , SER A:310 , ILE A:312 , GLN A:313 , ALA A:325 , PRO A:326 , GLY A:410 , ASN A:414 , HOH A:535 , HOH A:566 , HOH A:567
BINDING SITE FOR RESIDUE ADP A 499
02
AC2
SOFTWARE
ARG A:82 , GLU A:83 , TRP A:102 , TYR A:134 , ASP A:244 , GLN A:245 , PHE A:269
BINDING SITE FOR RESIDUE GOL A 500
03
AC3
SOFTWARE
ARG A:320 , TYR B:331 , LYS B:372
BINDING SITE FOR RESIDUE PO4 A 501
04
AC4
SOFTWARE
TYR A:331 , LYS A:372 , ARG B:320
BINDING SITE FOR RESIDUE PO4 A 502
05
AC5
SOFTWARE
LYS A:171 , GLY A:174 , LYS A:175 , TYR A:229 , HIS A:230
BINDING SITE FOR RESIDUE PO4 A 503
06
AC6
SOFTWARE
SER A:337 , THR A:338 , GLU A:381
BINDING SITE FOR RESIDUE CL A 504
07
AC7
SOFTWARE
GLY B:11 , THR B:12 , THR B:13 , ARG B:16 , GLY B:265 , THR B:266 , GLY B:309 , SER B:310 , ILE B:312 , GLN B:313 , ALA B:325 , PRO B:326 , GLY B:410 , ALA B:411 , LYS B:413 , ASN B:414 , HOH B:519
BINDING SITE FOR RESIDUE ADP B 499
08
AC8
SOFTWARE
ARG B:82 , GLU B:83 , TRP B:102 , TYR B:134 , ASP B:244 , GLN B:245 , PHE B:269
BINDING SITE FOR RESIDUE GOL B 500
09
AC9
SOFTWARE
LYS B:171 , GLY B:174 , LYS B:175 , ILE B:227 , TYR B:229 , HIS B:230
BINDING SITE FOR RESIDUE PO4 B 501
10
BC1
SOFTWARE
SER B:337 , THR B:338 , GLU B:381
BINDING SITE FOR RESIDUE CL B 502
11
BC2
SOFTWARE
GLY C:11 , THR C:12 , THR C:13 , ARG C:16 , GLY C:265 , THR C:266 , GLY C:309 , ILE C:312 , GLN C:313 , ALA C:325 , PRO C:326 , GLY C:410 , ALA C:411 , ASN C:414 , GOL C:500 , HOH C:510
BINDING SITE FOR RESIDUE ADP C 499
12
BC3
SOFTWARE
GLN C:81 , ARG C:82 , GLU C:83 , TRP C:102 , TYR C:134 , ASP C:244 , GLN C:245 , PHE C:269 , ADP C:499
BINDING SITE FOR RESIDUE GOL C 500
13
BC4
SOFTWARE
LYS C:171 , GLY C:174 , LYS C:175 , ILE C:227 , TYR C:229 , HIS C:230 , HOH C:547
BINDING SITE FOR RESIDUE PO4 C 501
14
BC5
SOFTWARE
SER C:337 , THR C:338 , GLU C:381
BINDING SITE FOR RESIDUE CL C 502
15
BC6
SOFTWARE
GLY D:11 , THR D:12 , ARG D:16 , GLY D:265 , THR D:266 , GLY D:309 , SER D:310 , ILE D:312 , ALA D:325 , PRO D:326 , GLY D:410 , ALA D:411 , LYS D:413 , ASN D:414 , HOH D:545
BINDING SITE FOR RESIDUE ADP D 499
16
BC7
SOFTWARE
GLN D:81 , ARG D:82 , GLU D:83 , TRP D:102 , TYR D:134 , ASP D:244 , GLN D:245 , PHE D:269
BINDING SITE FOR RESIDUE GOL D 500
17
BC8
SOFTWARE
ARG C:320 , TYR D:331 , LYS D:372
BINDING SITE FOR RESIDUE PO4 D 501
18
BC9
SOFTWARE
TYR C:331 , LYS C:372 , ARG D:320
BINDING SITE FOR RESIDUE PO4 D 502
19
CC1
SOFTWARE
LYS D:171 , GLY D:174 , LYS D:175 , ILE D:227 , TYR D:229 , HIS D:230 , HOH D:506
BINDING SITE FOR RESIDUE PO4 D 503
20
CC2
SOFTWARE
SER D:337 , THR D:338 , ARG D:377 , GLU D:381
BINDING SITE FOR RESIDUE CL D 504
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: FGGY_KINASES_2 (A:361-381,B:361-381,C:361-381,D:36...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FGGY_KINASES_2
PS00445
FGGY family of carbohydrate kinases signature 2.
GLPK_STAAC
361-381
4
A:361-381
B:361-381
C:361-381
D:361-381
[
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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
(1, 8)
Info
All SCOP Domains
1a: SCOP_d3ge1a1 (A:0-252)
1b: SCOP_d3ge1b1 (B:0-252)
1c: SCOP_d3ge1b2 (B:253-497)
1d: SCOP_d3ge1c1 (C:1-252)
1e: SCOP_d3ge1c2 (C:253-497)
1f: SCOP_d3ge1d1 (D:2-252)
1g: SCOP_d3ge1d2 (D:253-497)
1h: SCOP_d3ge1a2 (A:253-498)
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Protein Domains
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Organisms
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Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Ribonuclease H-like motif
(1424)
Superfamily
:
Actin-like ATPase domain
(426)
Family
:
automated matches
(111)
Protein domain
:
automated matches
(111)
Staphylococcus aureus [TaxId: 93062]
(2)
1a
d3ge1a1
A:0-252
1b
d3ge1b1
B:0-252
1c
d3ge1b2
B:253-497
1d
d3ge1c1
C:1-252
1e
d3ge1c2
C:253-497
1f
d3ge1d1
D:2-252
1g
d3ge1d2
D:253-497
1h
d3ge1a2
A:253-498
[
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
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Sorry, no Info available
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