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2DGL
Asym. Unit
Info
Asym.Unit (444 KB)
Biol.Unit 1 (438 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF ESCHERICHIA COLI GADB IN COMPLEX WITH BROMIDE
Authors
:
M. G. Gruetter, G. Capitani, H. Gut
Date
:
14 Mar 06 (Deposition) - 20 Jun 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.15
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Gadb Complexed With Bromide, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Gut, E. Pennacchietti, R. A. John, F. Bossa, G. Capitani, D. De Biase, M. G. Gruetter
Escherichia Coli Acid Resistance: Ph-Sensing, Activation By Chloride And Autoinhibition In Gadb
Embo J. V. 25 2643 2006
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 36)
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: BROMIDE ION (BRa)
2b: BROMIDE ION (BRb)
2c: BROMIDE ION (BRc)
2d: BROMIDE ION (BRd)
2e: BROMIDE ION (BRe)
2f: BROMIDE ION (BRf)
2g: BROMIDE ION (BRg)
2h: BROMIDE ION (BRh)
2i: BROMIDE ION (BRi)
2j: BROMIDE ION (BRj)
2k: BROMIDE ION (BRk)
2l: BROMIDE ION (BRl)
2m: BROMIDE ION (BRm)
2n: BROMIDE ION (BRn)
2o: BROMIDE ION (BRo)
2p: BROMIDE ION (BRp)
2q: BROMIDE ION (BRq)
2r: BROMIDE ION (BRr)
2s: BROMIDE ION (BRs)
2t: BROMIDE ION (BRt)
2u: BROMIDE ION (BRu)
2v: BROMIDE ION (BRv)
2w: BROMIDE ION (BRw)
2x: BROMIDE ION (BRx)
3a: PYRIDOXAL-5'-PHOSPHATE (PLPa)
3b: PYRIDOXAL-5'-PHOSPHATE (PLPb)
3c: PYRIDOXAL-5'-PHOSPHATE (PLPc)
3d: PYRIDOXAL-5'-PHOSPHATE (PLPd)
3e: PYRIDOXAL-5'-PHOSPHATE (PLPe)
3f: PYRIDOXAL-5'-PHOSPHATE (PLPf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACY
6
Ligand/Ion
ACETIC ACID
2
BR
24
Ligand/Ion
BROMIDE ION
3
PLP
6
Ligand/Ion
PYRIDOXAL-5'-PHOSPHATE
[
close Hetero Component info
]
Sites
(35, 35)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:16 , ARG F:427
BINDING SITE FOR RESIDUE BR A 467
02
AC2
SOFTWARE
ASN E:81 , ASP F:68 , HIS F:73
BINDING SITE FOR RESIDUE BR F 467
03
AC3
SOFTWARE
ARG A:17
BINDING SITE FOR RESIDUE BR A 468
04
AC4
SOFTWARE
SER B:16 , ARG C:427
BINDING SITE FOR RESIDUE BR B 467
05
AC5
SOFTWARE
TRP C:67 , ASP C:68 , HIS C:73
BINDING SITE FOR RESIDUE BR C 467
06
AC6
SOFTWARE
ARG B:17
BINDING SITE FOR RESIDUE BR B 468
07
AC7
SOFTWARE
ARG B:427 , SER C:16
BINDING SITE FOR RESIDUE BR B 469
08
AC8
SOFTWARE
ASN A:81 , ASP B:68 , HIS B:73
BINDING SITE FOR RESIDUE BR B 470
09
AC9
SOFTWARE
ARG C:17
BINDING SITE FOR RESIDUE BR C 468
10
BC1
SOFTWARE
SER D:16 , ARG E:427
BINDING SITE FOR RESIDUE BR D 467
11
BC2
SOFTWARE
ASP E:68 , HIS E:73 , ASN F:81
BINDING SITE FOR RESIDUE BR E 467
12
BC3
SOFTWARE
ARG D:17
BINDING SITE FOR RESIDUE BR D 468
13
BC4
SOFTWARE
ARG D:427 , SER E:16
BINDING SITE FOR RESIDUE BR E 468
14
BC5
SOFTWARE
ASN C:81 , ASP D:68 , HIS D:73
BINDING SITE FOR RESIDUE BR C 469
15
BC6
SOFTWARE
ARG E:17
BINDING SITE FOR RESIDUE BR E 469
16
BC7
SOFTWARE
ARG A:427 , SER F:16
BINDING SITE FOR RESIDUE BR F 468
17
BC8
SOFTWARE
ASP A:68 , HIS A:73 , ASN B:81
BINDING SITE FOR RESIDUE BR A 469
18
BC9
SOFTWARE
ARG F:17
BINDING SITE FOR RESIDUE BR F 469
19
CC1
SOFTWARE
ILE A:418
BINDING SITE FOR RESIDUE BR A 470
20
CC2
SOFTWARE
LYS B:381 , ILE B:418
BINDING SITE FOR RESIDUE BR B 471
21
CC3
SOFTWARE
LYS C:381 , ILE C:418
BINDING SITE FOR RESIDUE BR C 470
22
CC4
SOFTWARE
LYS D:381
BINDING SITE FOR RESIDUE BR D 469
23
CC5
SOFTWARE
ILE E:418
BINDING SITE FOR RESIDUE BR E 470
24
CC6
SOFTWARE
GLY A:125 , SER A:126 , SER A:127 , GLN A:163 , THR A:212 , ASP A:243 , ALA A:245 , SER A:273 , HIS A:275 , LYS A:276 , PHE B:317 , SER B:318
BINDING SITE FOR RESIDUE PLP A 500
25
CC7
SOFTWARE
PHE A:317 , SER A:318 , GLY B:125 , SER B:126 , SER B:127 , GLN B:163 , THR B:212 , ASP B:243 , ALA B:245 , SER B:273 , HIS B:275 , LYS B:276 , HOH B:567
BINDING SITE FOR RESIDUE PLP B 500
26
CC8
SOFTWARE
GLY C:125 , SER C:126 , SER C:127 , GLN C:163 , THR C:212 , ASP C:243 , ALA C:245 , SER C:273 , HIS C:275 , LYS C:276 , PHE D:317 , SER D:318
BINDING SITE FOR RESIDUE PLP C 501
27
CC9
SOFTWARE
PHE C:317 , SER C:318 , SER D:126 , SER D:127 , GLN D:163 , CYS D:165 , THR D:212 , ASP D:243 , ALA D:245 , SER D:273 , HIS D:275 , LYS D:276
BINDING SITE FOR RESIDUE PLP D 501
28
DC1
SOFTWARE
GLY E:125 , SER E:126 , SER E:127 , GLN E:163 , CYS E:165 , THR E:212 , ASP E:243 , ALA E:245 , SER E:273 , HIS E:275 , LYS E:276 , PHE F:317 , SER F:318
BINDING SITE FOR RESIDUE PLP E 502
29
DC2
SOFTWARE
PHE E:317 , SER E:318 , HOH E:529 , GLY F:125 , SER F:126 , SER F:127 , GLN F:163 , THR F:208 , THR F:212 , ASP F:243 , ALA F:245 , SER F:273 , HIS F:275 , LYS F:276
BINDING SITE FOR RESIDUE PLP F 502
30
DC3
SOFTWARE
THR E:62 , PHE E:63 , ASP F:86
BINDING SITE FOR RESIDUE ACY E 518
31
DC4
SOFTWARE
ASN E:83 , ASP E:86 , SER E:318 , THR F:62 , PHE F:63
BINDING SITE FOR RESIDUE ACY F 528
32
DC5
SOFTWARE
THR C:62 , PHE C:63 , ASP D:86 , SER D:318
BINDING SITE FOR RESIDUE ACY C 538
33
DC6
SOFTWARE
ASN C:83 , ASP C:86 , PHE C:317 , SER C:318 , THR D:62 , PHE D:63 , CYS D:64
BINDING SITE FOR RESIDUE ACY C 548
34
DC7
SOFTWARE
THR A:62 , PHE A:63 , CYS A:64 , ASN B:83 , ASP B:86
BINDING SITE FOR RESIDUE ACY B 558
35
DC8
SOFTWARE
ASN A:83 , ASP A:86 , SER A:318 , THR B:62 , PHE B:63
BINDING SITE FOR RESIDUE ACY A 568
[
close Site info
]
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, 6)
Info
All PROSITE Patterns/Profiles
1: DDC_GAD_HDC_YDC (A:269-290,B:269-290,C:269-290,D:26...)
;
View:
Select:
Label:
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
View:
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All Exon Boundaries
View:
Label:
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_d2dgla_ (A:)
1b: SCOP_d2dglb_ (B:)
1c: SCOP_d2dglc_ (C:)
1d: SCOP_d2dgld_ (D:)
1e: SCOP_d2dgle_ (E:)
1f: SCOP_d2dglf_ (F:)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
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
d2dgla_
A:
1b
d2dglb_
B:
1c
d2dglc_
C:
1d
d2dgld_
D:
1e
d2dgle_
E:
1f
d2dglf_
F:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Label:
Sorry, no Info available
[
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Protein & NOT Site
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Chain C
Chain D
Chain E
Chain F
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