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3COG
Asym. Unit
Info
Asym.Unit (271 KB)
Biol.Unit 1 (264 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN CYSTATHIONASE (CYSTATHIONINE GAMMA LYASE) IN COMPLEX WITH DL-PROPARGYLGLYCINE
Authors
:
R. Collins, T. Karlberg, L. Lehtio, C. H. Arrowsmith, H. Berglund, L. G. A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, I. Jo A. Kallas, T. Kotenyova, M. Moche, M. E. Nilsson, P. Nordlund, T. Nyman K. Olesen, C. Persson, H. Schuler, L. Svensson, A. G. Thorsell, L. Tres S. Van Den Berg, J. Sagermark, R. D. Busam, M. Welin, J. Weigelt, M. Wi Structural Genomics Consortium (Sgc)
Date
:
28 Mar 08 (Deposition) - 27 May 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Cth, Plp, Propargylglycine, Sgc, Inhibitor, Structural Genomics, Sgc Stockholm, Structural Genomics Consortium, Amino-Acid Biosynthesis, Cysteine Biosynthesis, Disease Mutation, Lyase, Phosphoprotein, Pyridoxal Phosphate
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Q. Sun, R. Collins, S. Huang, L. Holmberg-Schiavone, G. S. Anand, C. H. Tan, S. Van-Den-Berg, L. W. Deng, P. K. Moore, T. Karlberg, J. Sivaraman
Structural Basis For The Inhibition Mechanism Of Human Cystathionine Gamma-Lyase, An Enzyme Responsible For The Production Of H(2)S.
J. Biol. Chem. V. 284 3076 2009
[
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Hetero Components
(5, 15)
Info
All Hetero Components
1a: (2S)-2-AMINOPENT-4-ENOIC ACID (2AGa)
1b: (2S)-2-AMINOPENT-4-ENOIC ACID (2AGb)
1c: (2S)-2-AMINOPENT-4-ENOIC ACID (2AGc)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
3a: NITRATE ION (NO3a)
3b: NITRATE ION (NO3b)
3c: NITRATE ION (NO3c)
4a: DI(HYDROXYETHYL)ETHER (PEGa)
5a: PYRIDOXAL-5'-PHOSPHATE (PLPa)
5b: PYRIDOXAL-5'-PHOSPHATE (PLPb)
5c: PYRIDOXAL-5'-PHOSPHATE (PLPc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
2AG
3
Ligand/Ion
(2S)-2-AMINOPENT-4-ENOIC ACID
2
GOL
5
Ligand/Ion
GLYCEROL
3
NO3
3
Ligand/Ion
NITRATE ION
4
PEG
1
Ligand/Ion
DI(HYDROXYETHYL)ETHER
5
PLP
3
Ligand/Ion
PYRIDOXAL-5'-PHOSPHATE
[
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Sites
(15, 15)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR C:114 , ASN C:161 , LYS C:212 , SER C:340 , LEU C:341 , THR C:355 , ARG C:375
BINDING SITE FOR RESIDUE NO3 C 606
02
AC2
SOFTWARE
TYR D:114 , ASN D:161 , LYS D:212 , SER D:340 , LEU D:341 , THR D:355 , ARG D:375
BINDING SITE FOR RESIDUE NO3 D 607
03
AC3
SOFTWARE
TYR A:114 , ASN A:161 , LYS A:212 , SER A:340 , LEU A:341 , THR A:355 , ARG A:375
BINDING SITE FOR RESIDUE NO3 A 608
04
AC4
SOFTWARE
SER A:89 , GLY A:90 , LEU A:91 , TYR A:114 , ASN A:161 , ASP A:187 , THR A:189 , SER A:209 , THR A:211 , LYS A:212 , TYR B:60 , ARG B:62
BINDING SITE FOR RESIDUE PLP A 500
05
AC5
SOFTWARE
SER C:89 , GLY C:90 , LEU C:91 , TYR C:114 , ASN C:161 , ASP C:187 , THR C:189 , SER C:209 , THR C:211 , LYS C:212 , TYR D:60 , ARG D:62
BINDING SITE FOR RESIDUE PLP C 500
06
AC6
SOFTWARE
TYR C:60 , ARG C:62 , SER D:89 , GLY D:90 , LEU D:91 , TYR D:114 , ASN D:161 , ASP D:187 , SER D:209 , THR D:211 , LYS D:212 , LEU D:341
BINDING SITE FOR RESIDUE PLP D 500
07
AC7
SOFTWARE
TYR A:114 , ARG A:119 , GLU A:339 , TYR B:60 , ARG B:62
BINDING SITE FOR RESIDUE 2AG A 501
08
AC8
SOFTWARE
TYR C:114 , ARG C:119 , GLU C:339 , TYR D:60 , ARG D:62
BINDING SITE FOR RESIDUE 2AG C 501
09
AC9
SOFTWARE
GLU C:59 , TYR C:60 , ARG C:62 , TYR D:114 , ARG D:119 , GLU D:339
BINDING SITE FOR RESIDUE 2AG D 501
10
BC1
SOFTWARE
GLU C:127 , HIS D:99 , LEU D:100 , LEU D:101
BINDING SITE FOR RESIDUE GOL D 601
11
BC2
SOFTWARE
HIS C:99 , LEU C:100 , LEU C:101 , GLU D:127
BINDING SITE FOR RESIDUE GOL C 602
12
BC3
SOFTWARE
HIS A:99 , LEU A:100 , LEU A:101 , GLU B:127
BINDING SITE FOR RESIDUE GOL A 603
13
BC4
SOFTWARE
TRP B:32 , THR B:33 , SER B:34 , TRP D:32 , THR D:33 , SER D:34
BINDING SITE FOR RESIDUE GOL D 604
14
BC5
SOFTWARE
LEU C:43 , SER C:248 , PRO C:249 , ASP D:219 , ASP D:251
BINDING SITE FOR RESIDUE GOL D 605
15
BC6
SOFTWARE
PRO A:295 , HIS A:297 , PRO A:298 , GLN A:299 , HIS A:300 , GLU A:301 , LEU A:302 , ARG A:305
BINDING SITE FOR RESIDUE PEG A 609
[
close Site info
]
SAPs(SNPs)/Variants
(2, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_015450 (T67I, chain A/B/C/D, )
2: VAR_015451 (Q240E, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_015450
T
67
I
CGL_HUMAN
Disease (CSTNU)
28941785
A/B/C/D
T
67
I
2
UniProt
VAR_015451
Q
240
E
CGL_HUMAN
Disease (CSTNU)
28941786
A/B/C/D
Q
240
E
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: CYS_MET_METAB_PP (A:204-218,B:204-218,C:204-218,D:20...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CYS_MET_METAB_PP
PS00868
Cys/Met metabolism enzymes pyridoxal-phosphate attachment site.
CGL_HUMAN
204-218
4
A:204-218
B:204-218
C:204-218
D:204-218
[
close PROSITE info
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Exons
(12, 48)
Info
All Exons
Exon 1.1a (A:10-49 | B:10-56 | C:10-54 | D:10...)
Exon 1.2 (A:64-84 | B:57-84 | C:57-84 | D:57...)
Exon 1.3 (A:84-116 | B:84-116 | C:84-116 | D...)
Exon 1.4 (A:116-152 | B:116-152 | C:116-152 ...)
Exon 1.5 (A:153-196 | B:153-196 | C:153-196 ...)
Exon 1.6 (A:197-216 | B:197-216 | C:197-216 ...)
Exon 1.7 (A:216-242 | B:216-242 | C:216-242 ...)
Exon 1.8 (A:242-293 | B:242-293 | C:242-293 ...)
Exon 1.9 (A:293-333 | B:293-333 | C:293-333 ...)
Exon 1.10b (A:334-351 | B:334-351 | C:334-351 ...)
Exon 1.11 (A:351-397 | B:351-397 (gaps) | C:3...)
Exon 1.12d (A:398-399 | B:398-400 | C:398-401 ...)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1a
02: Boundary 1.1a/1.2
03: Boundary 1.2/1.3
04: Boundary 1.3/1.4
05: Boundary 1.4/1.5
06: Boundary 1.5/1.6
07: Boundary 1.6/1.7
08: Boundary 1.7/1.8
09: Boundary 1.8/1.9
10: Boundary 1.9/1.10b
11: Boundary 1.10b/1.11
12: Boundary 1.11/1.12d
13: Boundary 1.12d/-
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
1.1a
ENST00000370938
1a
ENSE00002195861
chr1:
70876955-70877266
312
CGL_HUMAN
1-56
56
4
A:10-49
B:10-56
C:10-54
D:10-56
40
47
45
47
1.2
ENST00000370938
2
ENSE00000798480
chr1:
70881639-70881720
82
CGL_HUMAN
57-84
28
4
A:64-84
B:57-84
C:57-84
D:57-84
21
28
28
28
1.3
ENST00000370938
3
ENSE00000798481
chr1:
70883620-70883715
96
CGL_HUMAN
84-116
33
4
A:84-116
B:84-116
C:84-116
D:84-116
33
33
33
33
1.4
ENST00000370938
4
ENSE00000774659
chr1:
70887249-70887358
110
CGL_HUMAN
116-152
37
4
A:116-152
B:116-152
C:116-152
D:116-152
37
37
37
37
1.5
ENST00000370938
5
ENSE00000774657
chr1:
70889968-70890099
132
CGL_HUMAN
153-196
44
4
A:153-196
B:153-196
C:153-196
D:153-196
44
44
44
44
1.6
ENST00000370938
6
ENSE00000798483
chr1:
70895477-70895534
58
CGL_HUMAN
197-216
20
4
A:197-216
B:197-216
C:197-216
D:197-216
20
20
20
20
1.7
ENST00000370938
7
ENSE00000798484
chr1:
70896000-70896077
78
CGL_HUMAN
216-242
27
4
A:216-242
B:216-242
C:216-242
D:216-242
27
27
27
27
1.8
ENST00000370938
8
ENSE00000798485
chr1:
70897766-70897918
153
CGL_HUMAN
242-293
52
4
A:242-293
B:242-293
C:242-293
D:242-293
52
52
52
52
1.9
ENST00000370938
9
ENSE00000774649
chr1:
70899511-70899632
122
CGL_HUMAN
293-333
41
4
A:293-333
B:293-333
C:293-333
D:293-333
41
41
41
41
1.10b
ENST00000370938
10b
ENSE00000774647
chr1:
70900808-70900860
53
CGL_HUMAN
334-351
18
4
A:334-351
B:334-351
C:334-351
D:334-351
18
18
18
18
1.11
ENST00000370938
11
ENSE00000774646
chr1:
70904371-70904509
139
CGL_HUMAN
351-397
47
4
A:351-397
B:351-397 (gaps)
C:351-397
D:351-397
47
47
47
47
1.12d
ENST00000370938
12d
ENSE00001829292
chr1:
70904784-70905253
470
CGL_HUMAN
398-405
8
4
A:398-399
B:398-400
C:398-401
D:398-401
2
3
4
4
[
close EXON info
]
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d3coga_ (A:)
1b: SCOP_d3cogb_ (B:)
1c: SCOP_d3cogc_ (C:)
1d: SCOP_d3cogd_ (D:)
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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
:
automated matches
(163)
Protein domain
:
automated matches
(163)
Human (Homo sapiens) [TaxId: 9606]
(17)
1a
d3coga_
A:
1b
d3cogb_
B:
1c
d3cogc_
C:
1d
d3cogd_
D:
[
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_3cogB01 (B:16-262)
1b: CATH_3cogD01 (D:16-262)
1c: CATH_3cogC01 (C:16-262)
1d: CATH_3cogA01 (A:16-262)
2a: CATH_3cogA02 (A:263-399)
2b: CATH_3cogC02 (C:263-401)
2c: CATH_3cogD02 (D:263-401)
2d: CATH_3cogB02 (B:263-400)
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Architectures
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Topologies
(
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(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Aspartate Aminotransferase; domain 2
(384)
Homologous Superfamily
:
Type I PLP-dependent aspartate aminotransferase-like (Major domain)
(384)
Human (Homo sapiens)
(18)
1a
3cogB01
B:16-262
1b
3cogD01
D:16-262
1c
3cogC01
C:16-262
1d
3cogA01
A:16-262
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Aspartate Aminotransferase, domain 1
(355)
Homologous Superfamily
:
Aspartate Aminotransferase, domain 1
(354)
Human (Homo sapiens)
(15)
2a
3cogA02
A:263-399
2b
3cogC02
C:263-401
2c
3cogD02
D:263-401
2d
3cogB02
B:263-400
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Asym.Unit (271 KB)
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