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2OKJ
Asym. Unit
Info
Asym.Unit (174 KB)
Biol.Unit 1 (167 KB)
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(1)
Title
:
THE X-RAY CRYSTAL STRUCTURE OF THE 67KDA ISOFORM OF GLUTAMIC ACID DECARBOXYLASE (GAD67)
Authors
:
A. M. Buckle, G. Fenalti, R. H. P. Law, J. C. Whisstock
Date
:
17 Jan 07 (Deposition) - 27 Mar 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Plp-Dependent Decarboxylase, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. Fenalti, R. H. P. Law, A. M. Buckle, C. Langendorf, K. Tuck, C. J. Rosado, N. G. Faux, K. Mahmood, C. S. Hampe, J. P. Banga, M. Wilce, J. Schmidberger, J. Rossjohn, O. El-Kabbani, R. N. Pike, A. I. Smith, I. R. Mackay, M. J. Rowley, J. C. Whisstock
Gaba Production By Glutamic Acid Decarboxylase Is Regulated By A Dynamic Catalytic Loop.
Nat. Struct. Mol. Biol. V. 14 280 2007
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 5)
Info
All Hetero Components
1a: GAMMA-AMINO-BUTANOIC ACID (ABUa)
1b: GAMMA-AMINO-BUTANOIC ACID (ABUb)
2a: 2-LYSINE(3-HYDROXY-2-METHYL-5-PHOS... (LLPa)
2b: 2-LYSINE(3-HYDROXY-2-METHYL-5-PHOS... (LLPb)
3a: 4-[({3-HYDROXY-2-METHYL-5-[(PHOSPH... (PLZa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ABU
2
Ligand/Ion
GAMMA-AMINO-BUTANOIC ACID
2
LLP
2
Mod. Amino Acid
2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
3
PLZ
1
Ligand/Ion
4-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]BUTANOIC ACID
[
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Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLN A:190 , LEU A:191 , SER A:192 , ARG A:567 , TYR B:434
BINDING SITE FOR RESIDUE ABU A 1001
2
AC2
SOFTWARE
LEU A:435 , ASN B:189 , GLN B:190 , LEU B:191 , SER B:192 , ARG B:567 , PLZ B:2001
BINDING SITE FOR RESIDUE ABU B 1002
3
AC3
SOFTWARE
PHE A:214 , CYS A:455 , GLY A:456 , GLN B:190 , LEU B:191 , SER B:192 , GLY B:251 , GLY B:252 , ALA B:253 , HIS B:291 , GLY B:346 , THR B:348 , ASP B:373 , ALA B:375 , ASN B:402 , HIS B:404 , LLP B:405 , ABU B:1002 , HOH B:2030 , HOH B:2035
BINDING SITE FOR RESIDUE PLZ B 2001
[
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SAPs(SNPs)/Variants
(4, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_018861 (I228L, chain A/B, )
2: VAR_011882 (V474G, chain A/B, )
3: VAR_011883 (R532Q, chain A/B, )
4: VAR_011884 (F565L, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_018861
I
228
L
DCE1_HUMAN
Polymorphism
45566933
A/B
I
228
L
2
UniProt
VAR_011882
V
474
G
DCE1_HUMAN
Polymorphism
769403
A/B
V
474
G
3
UniProt
VAR_011883
R
532
Q
DCE1_HUMAN
Polymorphism
769402
A/B
R
532
Q
4
UniProt
VAR_011884
F
565
L
DCE1_HUMAN
Polymorphism
1049736
A/B
F
565
L
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: DDC_GAD_HDC_YDC (A:398-419,B:398-419)
;
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.
DCE1_HUMAN
398-419
2
A:398-419
B:398-419
[
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]
Exons
(14, 28)
Info
All Exons
Exon 1.7d (A:93-102 | B:93-102)
Exon 1.8d (A:102-183 | B:102-183)
Exon 1.9 (A:183-213 | B:183-213)
Exon 1.11b (A:213-251 | B:213-251)
Exon 1.12b (A:251-289 | B:251-289)
Exon 1.13 (A:290-316 | B:290-316)
Exon 1.14 (A:316-334 | B:316-334)
Exon 1.15 (A:335-373 | B:335-373)
Exon 1.17b (A:374-395 | B:374-395)
Exon 1.18b (A:395-421 | B:395-421)
Exon 1.18c (A:422-471 | B:422-471)
Exon 1.19 (A:472-507 | B:472-507)
Exon 1.20 (A:508-537 | B:508-537)
Exon 1.21e (A:538-593 | B:538-594)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.6c/1.7d
02: Boundary 1.7d/1.8d
03: Boundary 1.8d/1.9
04: Boundary 1.9/1.11b
05: Boundary 1.11b/1.12b
06: Boundary 1.12b/1.13
07: Boundary 1.13/1.14
08: Boundary 1.14/1.15
09: Boundary 1.15/1.17b
10: Boundary 1.17b/1.18b
11: Boundary 1.18b/1.18c
12: Boundary 1.18c/1.19
13: Boundary 1.19/1.20
14: Boundary 1.20/1.21e
15: Boundary 1.21e/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.3a
ENST00000358196
3a
ENSE00001842698
chr2:
171673072-171673558
487
DCE1_HUMAN
-
0
0
-
-
1.5d
ENST00000358196
5d
ENSE00001338054
chr2:
171675039-171675183
145
DCE1_HUMAN
1-28
28
0
-
-
1.6c
ENST00000358196
6c
ENSE00000782079
chr2:
171678597-171678659
63
DCE1_HUMAN
28-49
22
0
-
-
1.7d
ENST00000358196
7d
ENSE00000782080
chr2:
171685985-171686143
159
DCE1_HUMAN
49-102
54
2
A:93-102
B:93-102
10
10
1.8d
ENST00000358196
8d
ENSE00000782081
chr2:
171687460-171687702
243
DCE1_HUMAN
102-183
82
2
A:102-183
B:102-183
82
82
1.9
ENST00000358196
9
ENSE00001629948
chr2:
171693303-171693393
91
DCE1_HUMAN
183-213
31
2
A:183-213
B:183-213
31
31
1.11b
ENST00000358196
11b
ENSE00001746727
chr2:
171700555-171700667
113
DCE1_HUMAN
213-251
39
2
A:213-251
B:213-251
39
39
1.12b
ENST00000358196
12b
ENSE00001746204
chr2:
171702016-171702131
116
DCE1_HUMAN
251-289
39
2
A:251-289
B:251-289
39
39
1.13
ENST00000358196
13
ENSE00001804749
chr2:
171702216-171702295
80
DCE1_HUMAN
290-316
27
2
A:290-316
B:290-316
27
27
1.14
ENST00000358196
14
ENSE00001689327
chr2:
171702519-171702573
55
DCE1_HUMAN
316-334
19
2
A:316-334
B:316-334
19
19
1.15
ENST00000358196
15
ENSE00001651804
chr2:
171704186-171704302
117
DCE1_HUMAN
335-373
39
2
A:335-373
B:335-373
39
39
1.17b
ENST00000358196
17b
ENSE00001671408
chr2:
171705796-171705860
65
DCE1_HUMAN
374-395
22
2
A:374-395
B:374-395
22
22
1.18b
ENST00000358196
18b
ENSE00001742181
chr2:
171709224-171709302
79
DCE1_HUMAN
395-421
27
2
A:395-421
B:395-421
27
27
1.18c
ENST00000358196
18c
ENSE00001701023
chr2:
171710383-171710532
150
DCE1_HUMAN
422-471
50
2
A:422-471
B:422-471
50
50
1.19
ENST00000358196
19
ENSE00001771447
chr2:
171713528-171713635
108
DCE1_HUMAN
472-507
36
2
A:472-507
B:472-507
36
36
1.20
ENST00000358196
20
ENSE00001676332
chr2:
171715314-171715403
90
DCE1_HUMAN
508-537
30
2
A:508-537
B:508-537
30
30
1.21e
ENST00000358196
21e
ENSE00001838008
chr2:
171716219-171717661
1443
DCE1_HUMAN
538-594
57
2
A:538-593
B:538-594
56
57
[
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SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
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Label:
Sorry, no Info available
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
[
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Pyridoxal_deC_2okjB01 (B:144-518)
1b: PFAM_Pyridoxal_deC_2okjB02 (B:144-518)
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Clans
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(
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(
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(
)
(
)
Clan
:
PLP_aminotran
(240)
Family
:
Pyridoxal_deC
(14)
Homo sapiens (Human)
(3)
1a
Pyridoxal_deC-2okjB01
B:144-518
1b
Pyridoxal_deC-2okjB02
B:144-518
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