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2DGM
Asym. Unit
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Asym.Unit (475 KB)
Biol.Unit 1 (468 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF ESCHERICHIA COLI GADB IN COMPLEX WITH IODIDE
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
:
1.95
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Gadb Complexed With Iodide, 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
(5, 53)
Info
All Hetero Components
1a: ACETIC ACID (ACYa)
2a: FORMIC ACID (FMTa)
2b: FORMIC ACID (FMTb)
2c: FORMIC ACID (FMTc)
2d: FORMIC ACID (FMTd)
2e: FORMIC ACID (FMTe)
2f: FORMIC ACID (FMTf)
2g: FORMIC ACID (FMTg)
2h: FORMIC ACID (FMTh)
2i: FORMIC ACID (FMTi)
2j: FORMIC ACID (FMTj)
2k: FORMIC ACID (FMTk)
2l: FORMIC ACID (FMTl)
2m: FORMIC ACID (FMTm)
3a: IODIDE ION (IODa)
3aa: IODIDE ION (IODaa)
3ab: IODIDE ION (IODab)
3ac: IODIDE ION (IODac)
3ad: IODIDE ION (IODad)
3ae: IODIDE ION (IODae)
3af: IODIDE ION (IODaf)
3b: IODIDE ION (IODb)
3c: IODIDE ION (IODc)
3d: IODIDE ION (IODd)
3e: IODIDE ION (IODe)
3f: IODIDE ION (IODf)
3g: IODIDE ION (IODg)
3h: IODIDE ION (IODh)
3i: IODIDE ION (IODi)
3j: IODIDE ION (IODj)
3k: IODIDE ION (IODk)
3l: IODIDE ION (IODl)
3m: IODIDE ION (IODm)
3n: IODIDE ION (IODn)
3o: IODIDE ION (IODo)
3p: IODIDE ION (IODp)
3q: IODIDE ION (IODq)
3r: IODIDE ION (IODr)
3s: IODIDE ION (IODs)
3t: IODIDE ION (IODt)
3u: IODIDE ION (IODu)
3v: IODIDE ION (IODv)
3w: IODIDE ION (IODw)
3x: IODIDE ION (IODx)
3y: IODIDE ION (IODy)
3z: IODIDE ION (IODz)
4a: DI(HYDROXYETHYL)ETHER (PEGa)
5a: PYRIDOXAL-5'-PHOSPHATE (PLPa)
5b: PYRIDOXAL-5'-PHOSPHATE (PLPb)
5c: PYRIDOXAL-5'-PHOSPHATE (PLPc)
5d: PYRIDOXAL-5'-PHOSPHATE (PLPd)
5e: PYRIDOXAL-5'-PHOSPHATE (PLPe)
5f: PYRIDOXAL-5'-PHOSPHATE (PLPf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACY
1
Ligand/Ion
ACETIC ACID
2
FMT
13
Ligand/Ion
FORMIC ACID
3
IOD
32
Ligand/Ion
IODIDE ION
4
PEG
1
Ligand/Ion
DI(HYDROXYETHYL)ETHER
5
PLP
6
Ligand/Ion
PYRIDOXAL-5'-PHOSPHATE
[
close Hetero Component info
]
Sites
(47, 47)
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)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
45: EC9 (SOFTWARE)
46: FC1 (SOFTWARE)
47: FC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:16 , ARG F:427
BINDING SITE FOR RESIDUE IOD A 2331
02
AC2
SOFTWARE
SER B:16 , ARG C:427
BINDING SITE FOR RESIDUE IOD B 2332
03
AC3
SOFTWARE
ARG B:427 , SER C:16
BINDING SITE FOR RESIDUE IOD B 2333
04
AC4
SOFTWARE
SER D:16 , ARG E:427
BINDING SITE FOR RESIDUE IOD D 2334
05
AC5
SOFTWARE
ARG D:427 , SER E:16
BINDING SITE FOR RESIDUE IOD E 2335
06
AC6
SOFTWARE
ARG A:427 , SER F:16
BINDING SITE FOR RESIDUE IOD F 2336
07
AC7
SOFTWARE
LYS A:381 , ILE A:418
BINDING SITE FOR RESIDUE IOD A 2337
08
AC8
SOFTWARE
ILE B:418
BINDING SITE FOR RESIDUE IOD B 2338
09
AC9
SOFTWARE
LYS C:381 , ILE C:418
BINDING SITE FOR RESIDUE IOD C 2339
10
BC1
SOFTWARE
ILE F:418
BINDING SITE FOR RESIDUE IOD F 2342
11
BC2
SOFTWARE
LYS A:453
BINDING SITE FOR RESIDUE IOD A 2343
12
BC3
SOFTWARE
LYS D:453
BINDING SITE FOR RESIDUE IOD D 2346
13
BC4
SOFTWARE
HIS E:451
BINDING SITE FOR RESIDUE IOD E 2347
14
BC5
SOFTWARE
LYS F:453
BINDING SITE FOR RESIDUE IOD F 2348
15
BC6
SOFTWARE
TRP A:67 , HIS A:73
BINDING SITE FOR RESIDUE IOD A 2349
16
BC7
SOFTWARE
ASN A:81 , ASP B:68 , HIS B:73
BINDING SITE FOR RESIDUE IOD B 2350
17
BC8
SOFTWARE
TRP C:67 , ASP C:68 , HIS C:73 , ASN D:81
BINDING SITE FOR RESIDUE IOD C 2351
18
BC9
SOFTWARE
ASN C:81 , ASP D:68 , HIS D:73
BINDING SITE FOR RESIDUE IOD D 2352
19
CC1
SOFTWARE
TRP E:67 , ASP E:68 , HIS E:73 , ASN F:81
BINDING SITE FOR RESIDUE IOD E 2353
20
CC2
SOFTWARE
HIS F:73
BINDING SITE FOR RESIDUE IOD F 2354
21
CC3
SOFTWARE
LEU A:382 , THR A:391 , LEU A:392
BINDING SITE FOR RESIDUE IOD A 2355
22
CC4
SOFTWARE
LEU B:382 , THR B:391 , LEU B:392
BINDING SITE FOR RESIDUE IOD B 2356
23
CC5
SOFTWARE
LEU C:382 , THR C:391 , LEU C:392
BINDING SITE FOR RESIDUE IOD C 2357
24
CC6
SOFTWARE
LEU D:382 , THR D:391 , LEU D:392
BINDING SITE FOR RESIDUE IOD D 2358
25
CC7
SOFTWARE
THR E:391 , LEU E:392
BINDING SITE FOR RESIDUE IOD E 2359
26
CC8
SOFTWARE
THR F:391 , LEU F:392
BINDING SITE FOR RESIDUE IOD F 2360
27
CC9
SOFTWARE
GLY A:125 , SER A:126 , SER A:127 , GLN A:163 , THR A:208 , THR A:212 , ASP A:243 , ALA A:245 , SER A:273 , HIS A:275 , LYS A:276 , HOH A:2651 , PHE B:317 , SER B:318 , HOH B:2680
BINDING SITE FOR RESIDUE PLP A 500
28
DC1
SOFTWARE
PHE A:317 , SER A:318 , HOH A:2637 , GLY B:125 , SER B:126 , SER B:127 , GLN B:163 , CYS B:165 , THR B:212 , ASP B:243 , ALA B:245 , SER B:273 , HIS B:275 , LYS B:276 , HOH B:2703
BINDING SITE FOR RESIDUE PLP B 500
29
DC2
SOFTWARE
GLY C:125 , SER C:126 , SER C:127 , GLN C:163 , THR C:208 , THR C:212 , ASP C:243 , ALA C:245 , SER C:273 , HIS C:275 , LYS C:276 , HOH C:2619 , PHE D:317 , SER D:318 , HOH D:2673
BINDING SITE FOR RESIDUE PLP C 501
30
DC3
SOFTWARE
PHE C:317 , SER C:318 , HOH C:2649 , GLY D:125 , 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 , HOH D:2649
BINDING SITE FOR RESIDUE PLP D 501
31
DC4
SOFTWARE
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:2857 , PHE F:317 , SER F:318 , HOH F:2688
BINDING SITE FOR RESIDUE PLP E 502
32
DC5
SOFTWARE
PHE E:317 , SER E:318 , HOH E:2869 , GLY F:125 , SER F:126 , SER F:127 , GLN F:163 , CYS F:165 , THR F:212 , ASP F:243 , ALA F:245 , SER F:273 , HIS F:275 , LYS F:276 , HOH F:2711
BINDING SITE FOR RESIDUE PLP F 502
33
DC6
SOFTWARE
ASN A:83 , ASP A:86 , THR B:62 , PHE B:63
BINDING SITE FOR RESIDUE FMT A 2550
34
DC7
SOFTWARE
THR A:62 , PHE A:63 , ASN B:83 , ASP B:86
BINDING SITE FOR RESIDUE FMT A 2560
35
DC8
SOFTWARE
ASN C:83 , ASP C:86 , THR D:62 , PHE D:63
BINDING SITE FOR RESIDUE FMT D 2570
36
DC9
SOFTWARE
THR C:62 , PHE C:63 , CYS C:64 , ASN D:83 , ASP D:86
BINDING SITE FOR RESIDUE FMT D 2580
37
EC1
SOFTWARE
ASN E:83 , ASP E:86 , THR F:62 , PHE F:63
BINDING SITE FOR RESIDUE FMT F 2590
38
EC2
SOFTWARE
TRP A:84 , ASP A:97 , THR A:121 , ASN A:122 , HOH A:2720
BINDING SITE FOR RESIDUE FMT A 2600
39
EC3
SOFTWARE
ASP C:97 , LEU C:98 , THR C:121 , ASN C:122 , HOH C:2725
BINDING SITE FOR RESIDUE FMT C 2610
40
EC4
SOFTWARE
TRP E:84 , ASP E:97 , THR E:121 , ASN E:122 , HOH E:2973
BINDING SITE FOR RESIDUE FMT E 2620
41
EC5
SOFTWARE
TRP D:84 , ASP D:97 , LEU D:98 , GLY D:120 , THR D:121 , ASN D:122 , HOH D:2778
BINDING SITE FOR RESIDUE FMT D 2630
42
EC6
SOFTWARE
TRP F:84 , ASP F:97 , THR F:121 , ASN F:122 , HOH F:2726
BINDING SITE FOR RESIDUE FMT F 2640
43
EC7
SOFTWARE
TRP B:84 , ASP B:97 , THR B:121 , ASN B:122 , HOH B:2707 , HOH B:2848
BINDING SITE FOR RESIDUE FMT B 2650
44
EC8
SOFTWARE
LEU F:98 , ALA F:118 , GLY F:120 , GLY F:311
BINDING SITE FOR RESIDUE FMT F 2660
45
EC9
SOFTWARE
PRO F:111 , ARG F:290 , ASP F:291 , HOH F:2678 , HOH F:2793 , HOH F:2810
BINDING SITE FOR RESIDUE FMT F 2670
46
FC1
SOFTWARE
THR E:62 , PHE E:63 , ASN F:83 , ASP F:86 , PHE F:317 , SER F:318
BINDING SITE FOR RESIDUE ACY E 2519
47
FC2
SOFTWARE
ASP E:228 , ASP E:237 , ASP E:239 , PRO E:265 , ARG E:266 , LYS E:268 , HOH E:2933 , HOH E:3104
BINDING SITE FOR RESIDUE PEG E 2833
[
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
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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
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
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Label:
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_d2dgma_ (A:)
1b: SCOP_d2dgmb_ (B:)
1c: SCOP_d2dgmc_ (C:)
1d: SCOP_d2dgmd_ (D:)
1e: SCOP_d2dgme_ (E:)
1f: SCOP_d2dgmf_ (F:)
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Protein Domains
(
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(
)
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
d2dgma_
A:
1b
d2dgmb_
B:
1c
d2dgmc_
C:
1d
d2dgmd_
D:
1e
d2dgme_
E:
1f
d2dgmf_
F:
[
close SCOP info
]
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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all PFAM domains
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Sorry, no Info available
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Chain B
Chain C
Chain D
Chain E
Chain F
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