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2NMP
Asym. Unit
Info
Asym.Unit (250 KB)
Biol.Unit 1 (241 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN CYSTATHIONINE GAMMA LYASE
Authors
:
T. Karlberg, J. Uppenberg, C. Arrowsmith, H. Berglund, R. D. Busam, R. C A. Edwards, U. B. Ericsson, S. Flodin, A. Flores, S. Graslund, B. M. Hal M. Hammarstrom, M. Hogbom, I. Johansson, T. Kotenyova, A. Magnusdott M. Moche, M. E. Nilsson, P. Nordlund, T. Nyman, D. Ogg, C. Persson, J. Sa P. Stenmark, M. Sundstrom, A. G. Thorsell, S. Van-Den-Berg, K. Wallde J. Weigelt, L. Holmberg-Schiavone, Structural Genomics Consorti
Date
:
23 Oct 06 (Deposition) - 07 Nov 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Amino-Acid Biosynthesis, Lyase, Pyridoxal Phopshate, Structural Genomics, Structural Genomics Consortium, Sgc
(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
(1, 3)
Info
All Hetero Components
1a: PYRIDOXAL-5'-PHOSPHATE (PLPa)
1b: PYRIDOXAL-5'-PHOSPHATE (PLPb)
1c: PYRIDOXAL-5'-PHOSPHATE (PLPc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
PLP
3
Ligand/Ion
PYRIDOXAL-5'-PHOSPHATE
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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
SER A:89 , GLY A:90 , LEU A:91 , TYR A:114 , GLU A:157 , 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
2
AC2
SOFTWARE
SER C:89 , GLY C:90 , LEU C:91 , TYR C:114 , GLU C:157 , ASN C:161 , ASP C:187 , SER C:209 , THR C:211 , LYS C:212 , TYR D:60 , ARG D:62
BINDING SITE FOR RESIDUE PLP C 500
3
AC3
SOFTWARE
TYR C:60 , ARG C:62 , SER D:89 , GLY D:90 , LEU D:91 , TYR D:114 , ASP D:187 , THR D:189 , SER D:209 , THR D:211 , LYS D:212
BINDING SITE FOR RESIDUE PLP D 500
[
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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)
[
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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
[
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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:
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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 (gaps)
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
[
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]
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2nmpa_ (A:)
1b: SCOP_d2nmpb_ (B:)
1c: SCOP_d2nmpc_ (C:)
1d: SCOP_d2nmpd_ (D:)
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Protein Domains
(
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(
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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
:
automated matches
(163)
Protein domain
:
automated matches
(163)
Human (Homo sapiens) [TaxId: 9606]
(17)
1a
d2nmpa_
A:
1b
d2nmpb_
B:
1c
d2nmpc_
C:
1d
d2nmpd_
D:
[
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_2nmpB01 (B:16-262)
1b: CATH_2nmpD01 (D:16-262)
1c: CATH_2nmpC01 (C:16-262)
1d: CATH_2nmpA01 (A:16-262)
2a: CATH_2nmpA02 (A:263-399)
2b: CATH_2nmpD02 (D:263-401)
2c: CATH_2nmpC02 (C:263-401)
2d: CATH_2nmpB02 (B:263-400)
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)
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)
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(
)
(
)
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
2nmpB01
B:16-262
1b
2nmpD01
D:16-262
1c
2nmpC01
C:16-262
1d
2nmpA01
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
2nmpA02
A:263-399
2b
2nmpD02
D:263-401
2c
2nmpC02
C:263-401
2d
2nmpB02
B:263-400
[
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Cys_Met_Meta_PP_2nmpD01 (D:19-395)
1b: PFAM_Cys_Met_Meta_PP_2nmpD02 (D:19-395)
1c: PFAM_Cys_Met_Meta_PP_2nmpD03 (D:19-395)
1d: PFAM_Cys_Met_Meta_PP_2nmpD04 (D:19-395)
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Clan
:
PLP_aminotran
(240)
Family
:
Cys_Met_Meta_PP
(15)
Homo sapiens (Human)
(1)
1a
Cys_Met_Meta_PP-2nmpD01
D:19-395
1b
Cys_Met_Meta_PP-2nmpD02
D:19-395
1c
Cys_Met_Meta_PP-2nmpD03
D:19-395
1d
Cys_Met_Meta_PP-2nmpD04
D:19-395
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