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Asym. Unit
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Asym.Unit (469 KB)
Biol.Unit 1 (462 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF ESCHERICHIA COLI GADB (NEUTRAL 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) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Neutral-Ph Form Of Gadb, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
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
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 24)
Info
All Hetero Components
1a: (5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-Y... (PLRa)
1b: (5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-Y... (PLRb)
1c: (5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-Y... (PLRc)
1d: (5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-Y... (PLRd)
1e: (5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-Y... (PLRe)
1f: (5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-Y... (PLRf)
2a: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSa)
2b: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSb)
2c: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSc)
2d: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSd)
2e: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSe)
2f: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSf)
2g: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSg)
2h: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSh)
2i: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSi)
2j: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSj)
2k: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSk)
2l: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSl)
2m: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSm)
2n: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSn)
2o: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSo)
2p: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSp)
2q: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSq)
2r: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSr)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
PLR
6
Ligand/Ion
(5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGENPHOSPHATE
2
TRS
18
Ligand/Ion
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
[
close Hetero Component info
]
Sites
(24, 24)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:125 , SER A:126 , SER A:127 , GLN A:163 , THR A:212 , ASP A:243 , ALA A:245 , HIS A:275 , LYS A:276 , HIS A:465 , THR A:466 , HOH A:3266 , HOH A:3314 , HOH A:3427 , PHE B:317 , SER B:318
BINDING SITE FOR RESIDUE PLR A 1500
02
AC2
SOFTWARE
PHE A:317 , SER A:318 , HOH A:3307 , 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 , HIS B:465 , HOH B:3316 , HOH B:3425
BINDING SITE FOR RESIDUE PLR B 1501
03
AC3
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 , HIS C:465 , THR C:466 , HOH C:3317 , HOH C:3326 , PHE D:317 , SER D:318 , HOH D:3310
BINDING SITE FOR RESIDUE PLR C 1502
04
AC4
SOFTWARE
PHE C:317 , SER C:318 , HOH C:3364 , GLY D:125 , SER D:126 , SER D:127 , GLN D:163 , THR D:212 , ASP D:243 , ALA D:245 , SER D:273 , HIS D:275 , LYS D:276 , HIS D:465 , THR D:466 , HOH D:3328 , HOH D:3422
BINDING SITE FOR RESIDUE PLR D 1503
05
AC5
SOFTWARE
SER E:126 , SER E:127 , GLN E:163 , THR E:212 , ASP E:243 , ALA E:245 , SER E:273 , HIS E:275 , LYS E:276 , HIS E:465 , THR E:466 , HOH E:3315 , HOH E:3319 , PHE F:317 , SER F:318 , HOH F:3295
BINDING SITE FOR RESIDUE PLR E 1504
06
AC6
SOFTWARE
PHE E:317 , SER E:318 , GLY F:125 , SER F:126 , SER F:127 , GLN F:163 , THR F:212 , ASP F:243 , ALA F:245 , SER F:273 , HIS F:275 , LYS F:276 , HIS F:465 , THR F:466 , HOH F:3267 , HOH F:3313 , HOH F:3318
BINDING SITE FOR RESIDUE PLR F 1505
07
AC7
SOFTWARE
GLN A:65 , THR A:66 , TRP A:67 , ASP A:69 , VAL A:72 , LEU A:279 , ALA A:280 , PRO A:281 , GLU A:330 , ARG A:427 , HOH A:3255 , HOH A:3305 , HOH A:3437 , ILE B:80 , ASN B:81
BINDING SITE FOR RESIDUE TRS A 3236
08
AC8
SOFTWARE
ILE A:80 , ASN A:81 , GLN B:65 , TRP B:67 , VAL B:72 , LEU B:279 , ALA B:280 , PRO B:281 , GLU B:330 , ARG B:427
BINDING SITE FOR RESIDUE TRS B 3237
09
AC9
SOFTWARE
ASN C:81 , GLN D:65 , TRP D:67 , ASP D:69 , VAL D:72 , LEU D:279 , GLU D:330 , ARG D:427 , HOH D:3363
BINDING SITE FOR RESIDUE TRS D 3238
10
BC1
SOFTWARE
GLN E:65 , THR E:66 , TRP E:67 , ASP E:69 , VAL E:72 , LEU E:279 , ALA E:280 , ARG E:427 , HOH E:3380 , HOH E:3437 , ASN F:81
BINDING SITE FOR RESIDUE TRS E 3239
11
BC2
SOFTWARE
ASN E:81 , GLN F:65 , TRP F:67 , VAL F:72 , LEU F:279 , ALA F:280 , PRO F:281 , GLU F:330 , ARG F:427 , HOH F:3286
BINDING SITE FOR RESIDUE TRS F 3240
12
BC3
SOFTWARE
VAL A:119 , GLY A:120 , THR A:121 , VAL A:300 , GLY A:311 , PHE A:313 , TRS A:3251 , HOH A:3372 , HOH A:3438
BINDING SITE FOR RESIDUE TRS A 3241
13
BC4
SOFTWARE
TRP B:84 , LYS B:87 , ASP B:97 , LEU B:98 , GLY B:120 , THR B:121 , ASN B:122 , HOH B:3390
BINDING SITE FOR RESIDUE TRS B 3242
14
BC5
SOFTWARE
TRP C:84 , LYS C:87 , ASP C:97 , GLY C:120 , THR C:121 , ASN C:122 , THR C:312 , HOH C:3442
BINDING SITE FOR RESIDUE TRS C 3243
15
BC6
SOFTWARE
TRP D:84 , ASP D:97 , LEU D:98 , VAL D:101 , GLY D:120 , THR D:121 , ASN D:122 , THR D:312 , TRS D:3245 , HOH D:3359
BINDING SITE FOR RESIDUE TRS D 3244
16
BC7
SOFTWARE
VAL D:119 , GLY D:120 , THR D:121 , GLY D:311 , THR D:312 , PHE D:313 , TRS D:3244
BINDING SITE FOR RESIDUE TRS D 3245
17
BC8
SOFTWARE
TRP E:84 , LYS E:87 , ASP E:97 , LEU E:98 , VAL E:101 , GLY E:120 , THR E:121 , ASN E:122 , THR E:312 , TRS E:3247
BINDING SITE FOR RESIDUE TRS E 3246
18
BC9
SOFTWARE
VAL E:119 , GLY E:120 , LEU E:295 , VAL E:300 , GLY E:311 , THR E:312 , PHE E:313 , TRS E:3246 , HOH E:3342 , HOH E:3410
BINDING SITE FOR RESIDUE TRS E 3247
19
CC1
SOFTWARE
TRP F:84 , ASP F:97 , LEU F:98 , VAL F:101 , GLY F:120 , THR F:121 , ASN F:122 , GLY F:311 , THR F:312 , TRS F:3249
BINDING SITE FOR RESIDUE TRS F 3248
20
CC2
SOFTWARE
VAL F:119 , GLY F:120 , THR F:121 , LEU F:295 , GLY F:311 , THR F:312 , PHE F:313 , TRS F:3248 , HOH F:3423 , HOH F:3438
BINDING SITE FOR RESIDUE TRS F 3249
21
CC3
SOFTWARE
GLN C:65 , TRP C:67 , ASP C:69 , VAL C:72 , LEU C:279 , ALA C:280 , PRO C:281 , GLU C:330 , HOH C:3399 , ASN D:81
BINDING SITE FOR RESIDUE TRS C 3250
22
CC4
SOFTWARE
TRP A:84 , ASP A:97 , LEU A:98 , VAL A:101 , GLY A:120 , THR A:121 , ASN A:122 , TRS A:3241 , HOH A:3288 , HOH A:3439
BINDING SITE FOR RESIDUE TRS A 3251
23
CC5
SOFTWARE
PRO A:91 , GLN A:92 , LEU B:52 , GLN C:58 , ARG C:402 , LEU C:436 , ASP C:440 , HOH C:3407
BINDING SITE FOR RESIDUE TRS C 3252
24
CC6
SOFTWARE
PRO E:184 , GLY E:185 , LEU E:187 , GLU E:364 , LYS E:381 , ILE E:418
BINDING SITE FOR RESIDUE TRS E 3253
[
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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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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
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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_d1pmoa_ (A:)
1b: SCOP_d1pmob_ (B:)
1c: SCOP_d1pmoc_ (C:)
1d: SCOP_d1pmod_ (D:)
1e: SCOP_d1pmoe_ (E:)
1f: SCOP_d1pmof_ (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
d1pmoa_
A:
1b
d1pmob_
B:
1c
d1pmoc_
C:
1d
d1pmod_
D:
1e
d1pmoe_
E:
1f
d1pmof_
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_1pmoF01 (F:33-383)
1b: PFAM_Pyridoxal_deC_1pmoF02 (F:33-383)
1c: PFAM_Pyridoxal_deC_1pmoF03 (F:33-383)
1d: PFAM_Pyridoxal_deC_1pmoF04 (F:33-383)
1e: PFAM_Pyridoxal_deC_1pmoF05 (F:33-383)
1f: PFAM_Pyridoxal_deC_1pmoF06 (F:33-383)
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(
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(
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(
)
Clan
:
PLP_aminotran
(240)
Family
:
Pyridoxal_deC
(14)
Escherichia coli (strain K12)
(3)
1a
Pyridoxal_deC-1pmoF01
F:33-383
1b
Pyridoxal_deC-1pmoF02
F:33-383
1c
Pyridoxal_deC-1pmoF03
F:33-383
1d
Pyridoxal_deC-1pmoF04
F:33-383
1e
Pyridoxal_deC-1pmoF05
F:33-383
1f
Pyridoxal_deC-1pmoF06
F:33-383
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Asym.Unit (469 KB)
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