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1BU6
Asym. Unit
Info
Asym.Unit (327 KB)
Biol.Unit 1 (320 KB)
Biol.Unit 2 (163 KB)
Biol.Unit 3 (164 KB)
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(1)
Title
:
CRYSTAL STRUCTURES OF ESCHERICHIA COLI GLYCEROL KINASE AND THE MUTANT A65T IN AN INACTIVE TETRAMER: CONFORMATIONAL CHANGES AND IMPLICATIONS FOR ALLOSTERIC REGULATION
Authors
:
M. D. Feese, H. R. Faber, C. E. Bystrom, D. W. Pettigrew, S. J. Remington
Date
:
30 Aug 98 (Deposition) - 16 Sep 98 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.37
Chains
:
Asym. Unit : O,X,Y,Z
Biol. Unit 1: O,X,Y,Z (1x)
Biol. Unit 2: O,Y (1x)
Biol. Unit 3: X,Z (1x)
Keywords
:
Allostery, Cooperativity, Glycerol Kinase, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. D. Feese, H. R. Faber, C. E. Bystrom, D. W. Pettigrew, S. J. Remington
Glycerol Kinase From Escherichia Coli And An Ala65-->Thr Mutant: The Crystal Structures Reveal Conformational Change With Implications For Allosteric Regulation.
Structure V. 6 1407 1998
(for further references see the
PDB file header
)
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Hetero Components
(2, 10)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
4
Ligand/Ion
GLYCEROL
2
SO4
6
Ligand/Ion
SULFATE ION
[
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Sites
(11, 11)
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: SO4 (AUTHOR)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN O:228 , GLY O:233 , GLY O:234 , ARG O:236 , HOH O:505 , GLY X:233 , GLY X:234 , ARG X:236 , HOH X:506 , ARG Z:236
BINDING SITE FOR RESIDUE SO4 O 502
02
AC2
SOFTWARE
ARG O:236 , GLY Y:233 , GLY Y:234 , ARG Y:236 , GLY Z:233 , GLY Z:234 , ARG Z:236
BINDING SITE FOR RESIDUE SO4 Z 502
03
AC3
SOFTWARE
GLY O:12 , THR O:13 , THR O:14 , ARG O:17 , THR O:267
BINDING SITE FOR RESIDUE SO4 O 503
04
AC4
SOFTWARE
GLY Y:12 , THR Y:13 , THR Y:14 , ASP Y:245 , THR Y:267 , GOL Y:503
BINDING SITE FOR RESIDUE SO4 Y 502
05
AC5
SOFTWARE
GLY Z:12 , THR Z:13 , ARG Z:17 , ASP Z:245 , THR Z:267 , HOH Z:513
BINDING SITE FOR RESIDUE SO4 Z 503
06
AC6
SOFTWARE
GLY X:12 , THR X:13 , ARG X:17 , ASP X:245 , THR X:267 , GOL X:503 , HOH X:513 , HOH X:526
BINDING SITE FOR RESIDUE SO4 X 502
07
AC7
SOFTWARE
ARG O:83 , GLU O:84 , TRP O:103 , TYR O:135 , ASP O:245 , GLN O:246
BINDING SITE FOR RESIDUE GOL O 504
08
AC8
SOFTWARE
GLN Y:82 , ARG Y:83 , GLU Y:84 , TRP Y:103 , TYR Y:135 , ASP Y:245 , GLN Y:246 , SO4 Y:502 , HOH Y:527
BINDING SITE FOR RESIDUE GOL Y 503
09
AC9
SOFTWARE
GLN Z:82 , ARG Z:83 , GLU Z:84 , TRP Z:103 , TYR Z:135 , ASP Z:245 , GLN Z:246 , PHE Z:270
BINDING SITE FOR RESIDUE GOL Z 504
10
BC1
SOFTWARE
GLN X:82 , ARG X:83 , GLU X:84 , TRP X:103 , TYR X:135 , ASP X:245 , GLN X:246 , SO4 X:502
BINDING SITE FOR RESIDUE GOL X 503
11
SO4
AUTHOR
ARG O:236
SULPHATE BINDING SITE. RESIDUES 230 - 236: THIS REGION IS DISORDERED IN PREVIOUSLY SOLVED CRYSTAL STRUCTURES OF GLYCEROL KINASE, BUT IS ORDERED IN THIS STRUCTURE AND FORMS A SULPHATE BINDING SITE AT THE 2-FOLD DIMER-DIMER INTERFACE. THIS SITE IS PROPOSED TO BE PART OF THE BINDING SITE FOR THE ALLOSTERIC EFFECTOR FBP (SEE REF. FOR THIS STRUCTURE).
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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
(2, 8)
Info
All PROSITE Patterns/Profiles
1: FGGY_KINASES_1 (O:135-147,X:135-147,Y:135-147,Z:13...)
2: FGGY_KINASES_2 (O:362-382,X:362-382,Y:362-382,Z:36...)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FGGY_KINASES_1
PS00933
FGGY family of carbohydrate kinases signature 1.
GLPK_ECOLI
136-148
4
O:135-147
X:135-147
Y:135-147
Z:135-147
2
FGGY_KINASES_2
PS00445
FGGY family of carbohydrate kinases signature 2.
GLPK_ECOLI
363-383
4
O:362-382
X:362-382
Y:362-382
Z:362-382
[
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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.
SCOP Domains
(1, 8)
Info
All SCOP Domains
1a: SCOP_d1bu6o1 (O:3-253)
1b: SCOP_d1bu6o2 (O:254-499)
1c: SCOP_d1bu6x1 (X:3-253)
1d: SCOP_d1bu6x2 (X:254-500)
1e: SCOP_d1bu6y1 (Y:2-253)
1f: SCOP_d1bu6y2 (Y:254-500)
1g: SCOP_d1bu6z1 (Z:3-253)
1h: SCOP_d1bu6z2 (Z:254-500)
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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
:
Glycerol kinase
(21)
Protein domain
:
Glycerol kinase
(21)
Escherichia coli [TaxId: 562]
(13)
1a
d1bu6o1
O:3-253
1b
d1bu6o2
O:254-499
1c
d1bu6x1
X:3-253
1d
d1bu6x2
X:254-500
1e
d1bu6y1
Y:2-253
1f
d1bu6y2
Y:254-500
1g
d1bu6z1
Z:3-253
1h
d1bu6z2
Z:254-500
[
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1bu6O02 (O:254-499)
1b: CATH_1bu6Z02 (Z:254-500)
1c: CATH_1bu6O01 (O:3-253)
1d: CATH_1bu6Z01 (Z:3-253)
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Organisms
(
)
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)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Nucleotidyltransferase; domain 5
(788)
Homologous Superfamily
:
[code=3.30.420.40, no name defined]
(217)
Escherichia coli. Organism_taxid: 562.
(5)
1a
1bu6O02
O:254-499
1b
1bu6Z02
Z:254-500
1c
1bu6O01
O:3-253
1d
1bu6Z01
Z:3-253
[
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Pfam Domains
(0, 0)
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all PFAM domains
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Asymmetric Unit 1
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select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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Show PDB file:
Asym.Unit (327 KB)
Header - Asym.Unit
Biol.Unit 1 (320 KB)
Header - Biol.Unit 1
Biol.Unit 2 (163 KB)
Header - Biol.Unit 2
Biol.Unit 3 (164 KB)
Header - Biol.Unit 3
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