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1PMM
Asym. Unit
Info
Asym.Unit (468 KB)
Biol.Unit 1 (462 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF ESCHERICHIA COLI GADB (LOW PH)
Authors
:
G. Capitani, D. De Biase, C. Aurizi, H. Gut, F. Bossa, M. G. Grutter
Date
:
11 Jun 03 (Deposition) - 17 Feb 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Low-Ph Form Of Gadb, Lyase
(Keyword Search:
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Reference
:
G. Capitani, D. De Biase, C. Aurizi, H. Gut, F. Bossa, M. G. Grutter
Crystal Structure And Functional Analysis Of Escherichia Coli Glutamate Decarboxylase
Embo J. V. 22 4027 2003
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Hetero Components
(2, 12)
Info
All Hetero Components
1a: ACETIC ACID (ACYa)
1b: ACETIC ACID (ACYb)
1c: ACETIC ACID (ACYc)
1d: ACETIC ACID (ACYd)
1e: ACETIC ACID (ACYe)
1f: ACETIC ACID (ACYf)
2a: PYRIDOXAL-5'-PHOSPHATE (PLPa)
2b: PYRIDOXAL-5'-PHOSPHATE (PLPb)
2c: PYRIDOXAL-5'-PHOSPHATE (PLPc)
2d: PYRIDOXAL-5'-PHOSPHATE (PLPd)
2e: PYRIDOXAL-5'-PHOSPHATE (PLPe)
2f: PYRIDOXAL-5'-PHOSPHATE (PLPf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACY
6
Ligand/Ion
ACETIC ACID
2
PLP
6
Ligand/Ion
PYRIDOXAL-5'-PHOSPHATE
[
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Sites
(12, 12)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:125 , SER A:126 , SER A:127 , GLN A:163 , CYS A:165 , THR A:208 , THR A:212 , ASP A:243 , ALA A:245 , SER A:273 , HIS A:275 , LYS A:276 , HOH A:5552 , HOH A:5567 , PHE B:317 , SER B:318
BINDING SITE FOR RESIDUE PLP A 500
02
AC2
SOFTWARE
PHE A:317 , SER A:318 , GLY B:125 , SER B:126 , SER B:127 , GLN B:163 , CYS B:165 , THR B:208 , THR B:212 , ASP B:243 , ALA B:245 , SER B:273 , HIS B:275 , LYS B:276 , HOH B:6552 , HOH B:6574
BINDING SITE FOR RESIDUE PLP B 500
03
AC3
SOFTWARE
GLY C:125 , SER C:126 , SER C:127 , GLN C:163 , CYS C:165 , THR C:208 , THR C:212 , ASP C:243 , ALA C:245 , SER C:273 , HIS C:275 , LYS C:276 , HOH C:8528 , PHE D:317 , SER D:318 , HOH D:7561
BINDING SITE FOR RESIDUE PLP C 501
04
AC4
SOFTWARE
PHE C:317 , SER C:318 , GLY D:125 , SER D:126 , SER D:127 , GLN D:163 , CYS D:165 , THR D:208 , THR D:212 , ASP D:243 , ALA D:245 , SER D:273 , HIS D:275 , LYS D:276 , HOH D:7538 , HOH D:7566
BINDING SITE FOR RESIDUE PLP D 501
05
AC5
SOFTWARE
GLY E:125 , SER E:126 , SER E:127 , GLN E:163 , CYS E:165 , THR E:208 , THR E:212 , ASP E:243 , ALA E:245 , SER E:273 , HIS E:275 , LYS E:276 , HOH E:9548 , PHE F:317 , SER F:318 , HOH F:520
BINDING SITE FOR RESIDUE PLP E 502
06
AC6
SOFTWARE
PHE E:317 , SER E:318 , HOH E:9562 , GLY F:125 , SER F:126 , SER F:127 , GLN F:163 , CYS F:165 , THR F:208 , THR F:212 , ASP F:243 , ALA F:245 , SER F:273 , HIS F:275 , LYS F:276 , HOH F:544
BINDING SITE FOR RESIDUE PLP F 502
07
AC7
SOFTWARE
ASN A:83 , ASP A:86 , PHE A:317 , SER A:318 , HOH A:5654 , THR B:62 , PHE B:63
BINDING SITE FOR RESIDUE ACY A 5518
08
AC8
SOFTWARE
THR A:62 , PHE A:63 , ASN B:83 , ASP B:86 , SER B:318 , HOH B:6689
BINDING SITE FOR RESIDUE ACY B 6518
09
AC9
SOFTWARE
ASN C:83 , ASP C:86 , SER C:318 , THR D:62 , PHE D:63
BINDING SITE FOR RESIDUE ACY D 7518
10
BC1
SOFTWARE
THR C:62 , PHE C:63 , HOH C:8740 , ASN D:83 , ASP D:86 , SER D:318
BINDING SITE FOR RESIDUE ACY C 8518
11
BC2
SOFTWARE
ASN E:83 , ASP E:86 , SER E:318 , HOH E:9537 , THR F:62 , PHE F:63
BINDING SITE FOR RESIDUE ACY E 9518
12
BC3
SOFTWARE
THR E:62 , PHE E:63 , HOH E:9678 , ASN F:83 , ASP F:86 , SER F:318
BINDING SITE FOR RESIDUE ACY E 9519
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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
(1, 6)
Info
All PROSITE Patterns/Profiles
1: DDC_GAD_HDC_YDC (A:269-290,B:269-290,C:269-290,D:26...)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DDC_GAD_HDC_YDC
PS00392
DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site.
DCEB_ECOLI
269-290
6
A:269-290
B:269-290
C:269-290
D:269-290
E:269-290
F:269-290
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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, 6)
Info
All SCOP Domains
1a: SCOP_d1pmma_ (A:)
1b: SCOP_d1pmmb_ (B:)
1c: SCOP_d1pmmc_ (C:)
1d: SCOP_d1pmmd_ (D:)
1e: SCOP_d1pmme_ (E:)
1f: SCOP_d1pmmf_ (F:)
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Protein Domains
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Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
PLP-dependent transferase-like
(627)
Superfamily
:
PLP-dependent transferases
(625)
Family
:
Pyridoxal-dependent decarboxylase
(14)
Protein domain
:
Glutamate decarboxylase beta, GadB
(8)
Escherichia coli [TaxId: 562]
(5)
1a
d1pmma_
A:
1b
d1pmmb_
B:
1c
d1pmmc_
C:
1d
d1pmmd_
D:
1e
d1pmme_
E:
1f
d1pmmf_
F:
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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
(1, 6)
Info
all PFAM domains
1a: PFAM_Pyridoxal_deC_1pmmF01 (F:33-383)
1b: PFAM_Pyridoxal_deC_1pmmF02 (F:33-383)
1c: PFAM_Pyridoxal_deC_1pmmF03 (F:33-383)
1d: PFAM_Pyridoxal_deC_1pmmF04 (F:33-383)
1e: PFAM_Pyridoxal_deC_1pmmF05 (F:33-383)
1f: PFAM_Pyridoxal_deC_1pmmF06 (F:33-383)
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Clan
:
PLP_aminotran
(240)
Family
:
Pyridoxal_deC
(14)
Escherichia coli (strain K12)
(3)
1a
Pyridoxal_deC-1pmmF01
F:33-383
1b
Pyridoxal_deC-1pmmF02
F:33-383
1c
Pyridoxal_deC-1pmmF03
F:33-383
1d
Pyridoxal_deC-1pmmF04
F:33-383
1e
Pyridoxal_deC-1pmmF05
F:33-383
1f
Pyridoxal_deC-1pmmF06
F:33-383
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