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2VD6
Biol. Unit 1
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Asym.Unit (321 KB)
Biol.Unit 1 (313 KB)
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(1)
Title
:
HUMAN ADENYLOSUCCINATE LYASE IN COMPLEX WITH ITS SUBSTRATE N6-(1,2-DICARBOXYETHYL)-AMP, AND ITS PRODUCTS AMP AND FUMARATE.
Authors
:
P. Stenmark, M. Moche, C. Arrowsmith, H. Berglund, R. Busam, R. Collins L. G. Dahlgren, A. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hamma B. M. Hallberg, L. Holmberg-Schiavone, I. Johansson, A. Kallas, T. Ka T. Kotenyova, L. Lehtio, M. Nilsson, T. Nyman, D. Ogg, C. Persson, J. Sa M. Sundstrom, A. G. Thorsell, L. Tresaugues, S. Van Den Berg, J. Weig M. Welin, P. Nordlund, Structural Genomics Consortium (Sgc)
Date
:
30 Sep 07 (Deposition) - 23 Oct 07 (Release) - 18 Jul 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Purine Biosynthesis, Lyase, Epilepsy, Purine Metabolism
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Stenmark, M. Moche, C. Arrowsmith, H. Berglund, R. Busam, R. Collins, L. G. Dahlgren, A. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, B. M. Hallberg, L. Holmberg-Schiavone, I. Johansson, A. Kallas, T. Karlberg, T. Kotenyova, L. Lehtio, M. Nilsson, T. Nyman, D. Ogg, C. Persson, J. Sagemark, M. Sundstrom, A. G. Thorsell, L. Tresaugues, S. Van Den Berg, J. Weigelt, M. Welin, P. Nordlund
Human Adenylosuccinate Lyase In Complex With Its Substrate N6-(1, 2-Dicarboxyethyl)-Amp, And Its Products Amp And Fumarate.
To Be Published
[
close entry info
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Hetero Components
(4, 11)
Info
All Hetero Components
1a: 2-[9-(3,4-DIHYDROXY-5-PHOSPHONOOXY... (2SAa)
1b: 2-[9-(3,4-DIHYDROXY-5-PHOSPHONOOXY... (2SAb)
2a: ADENOSINE MONOPHOSPHATE (AMPa)
2b: ADENOSINE MONOPHOSPHATE (AMPb)
3a: CHLORIDE ION (CLa)
3b: CHLORIDE ION (CLb)
3c: CHLORIDE ION (CLc)
3d: CHLORIDE ION (CLd)
3e: CHLORIDE ION (CLe)
3f: CHLORIDE ION (CLf)
3g: CHLORIDE ION (CLg)
4a: FUMARIC ACID (FUMa)
4b: FUMARIC ACID (FUMb)
5a: GLYCEROL (GOLa)
5b: GLYCEROL (GOLb)
5c: GLYCEROL (GOLc)
5d: GLYCEROL (GOLd)
5e: GLYCEROL (GOLe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
2SA
2
Ligand/Ion
2-[9-(3,4-DIHYDROXY-5-PHOSPHONOOXYMETHYL-TETRAHYDRO-FURAN-2-YL)-9H-PURIN-6-YLAMINO]-SUCCINIC ACID
2
AMP
2
Ligand/Ion
ADENOSINE MONOPHOSPHATE
3
CL
-1
Ligand/Ion
CHLORIDE ION
4
FUM
2
Ligand/Ion
FUMARIC ACID
5
GOL
5
Ligand/Ion
GLYCEROL
[
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Sites
(18, 18)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:85 , HIS A:86 , ASP A:87 , SER A:112 , GLN A:241 , ARG A:329 , LEU A:331 , SER A:334 , ALA A:335 , ARG A:338 , FUM A:1001 , CL A:2001 , HOH A:2054 , HOH A:2251 , HOH A:2252 , HOH A:2253 , HIS B:159 , ARG D:20 , TYR D:21 , MET D:299 , ARG D:303
BINDING SITE FOR RESIDUE AMP A1000
02
AC2
SOFTWARE
HIS A:86 , MET A:89 , THR A:111 , SER A:112 , GLN A:241 , AMP A:1000 , HOH A:2255 , HOH A:2256 , THR B:158 , HIS B:159 , LYS D:295
BINDING SITE FOR RESIDUE FUM A1001
03
AC3
SOFTWARE
LYS A:35 , TRP A:39 , ASP A:87 , GLY A:116 , ASP A:120 , SER A:334 , ARG A:338 , HOH A:2161 , HOH A:2257
BINDING SITE FOR RESIDUE GOL A1003
04
AC4
SOFTWARE
AMP A:1000 , ASN D:297 , MET D:299
BINDING SITE FOR RESIDUE CL A2001
05
AC5
SOFTWARE
THR A:111 , TYR A:114 , ARG A:196 , LYS A:199 , GLY A:200
BINDING SITE FOR RESIDUE CL A2002
06
AC6
SOFTWARE
THR A:158 , HIS A:159 , ARG B:85 , HIS B:86 , ASP B:87 , THR B:111 , SER B:112 , GLN B:241 , ARG B:329 , SER B:334 , ALA B:335 , ARG B:338 , CL B:2001 , HOH B:2038 , HOH B:2051 , HOH B:2130 , HOH B:2161 , HOH B:2163 , HOH B:2165 , HOH B:2166 , ARG C:20 , TYR C:21 , LYS C:295 , MET C:299 , ARG C:303
BINDING SITE FOR RESIDUE 2SA B1002
07
AC7
SOFTWARE
LYS B:35 , ASP B:87 , GLY B:116 , ASP B:120 , SER B:334 , ARG B:338 , HOH B:2168
BINDING SITE FOR RESIDUE GOL B1003
08
AC8
SOFTWARE
ASP B:120 , ARG B:337 , ARG B:338 , LEU B:341 , ALA B:342 , HOH B:2131
BINDING SITE FOR RESIDUE GOL B1004
09
AC9
SOFTWARE
2SA B:1002 , HOH B:2166 , ASN C:297
BINDING SITE FOR RESIDUE CL B2001
10
BC1
SOFTWARE
THR B:111 , TYR B:114 , ARG B:196 , LYS B:199 , GLY B:200
BINDING SITE FOR RESIDUE CL B2002
11
BC2
SOFTWARE
ARG B:20 , TYR B:21 , MET B:299 , ARG B:303 , ARG C:85 , HIS C:86 , ASP C:87 , SER C:112 , GLN C:241 , ARG C:329 , LEU C:331 , SER C:334 , ALA C:335 , ARG C:338 , FUM C:1001 , HOH C:2241 , HOH C:2242 , HOH C:2243 , HIS D:159
BINDING SITE FOR RESIDUE AMP C1000
12
BC3
SOFTWARE
LYS B:295 , ASN B:297 , HIS C:86 , THR C:111 , SER C:112 , GLN C:241 , AMP C:1000 , THR D:158 , HIS D:159
BINDING SITE FOR RESIDUE FUM C1001
13
BC4
SOFTWARE
LYS C:35 , TRP C:39 , ASP C:87 , GLY C:116 , ASP C:120 , SER C:334 , ARG C:338 , HOH C:2167 , HOH C:2245
BINDING SITE FOR RESIDUE GOL C1003
14
BC5
SOFTWARE
TYR C:114 , ARG C:196 , LYS C:199 , GLY C:200
BINDING SITE FOR RESIDUE CL C2002
15
BC6
SOFTWARE
ARG A:20 , TYR A:21 , LYS A:295 , MET A:299 , ARG A:303 , THR C:158 , HIS C:159 , ARG D:85 , HIS D:86 , ASP D:87 , THR D:111 , SER D:112 , GLN D:241 , ARG D:329 , SER D:334 , ALA D:335 , ARG D:338 , CL D:2001 , HOH D:2067 , HOH D:2087 , HOH D:2244 , HOH D:2245 , HOH D:2246 , HOH D:2247 , HOH D:2249
BINDING SITE FOR RESIDUE 2SA D1002
16
BC7
SOFTWARE
LYS D:35 , TRP D:39 , ASP D:87 , GLY D:116 , ASP D:120 , SER D:334 , ARG D:338 , HOH D:2212 , HOH D:2213 , HOH D:2250
BINDING SITE FOR RESIDUE GOL D1003
17
BC8
SOFTWARE
ASN A:297 , MET A:299 , 2SA D:1002 , HOH D:2026
BINDING SITE FOR RESIDUE CL D2001
18
BC9
SOFTWARE
THR D:111 , TYR D:114 , ARG D:196 , LYS D:199 , GLY D:200
BINDING SITE FOR RESIDUE CL D2002
[
close Site info
]
SAPs(SNPs)/Variants
(27, 108)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_016931 (M26L, chain A/B/C/D, )
02: VAR_037883 (S31N, chain A/B/C/D, )
03: VAR_007972 (I72V, chain A/B/C/D, )
04: VAR_017079 (P100A, chain A/B/C/D, )
05: VAR_017080 (Y114H, chain A/B/C/D, )
06: VAR_007973 (R141W, chain A/B/C/D, )
07: VAR_037884 (K147M, chain A/B/C/D, )
08: VAR_007974 (R190Q, chain A/B/C/D, )
09: VAR_017081 (R194C, chain A/B/C/D, )
10: VAR_007975 (K246E, chain A/B/C/D, )
11: VAR_017082 (D268N, chain A/B/C/D, )
12: VAR_007976 (R303C, chain A/B/C/D, )
13: VAR_017083 (L311V, chain A/B/C/D, )
14: VAR_017084 (P318L, chain A/B/C/D, )
15: VAR_017085 (V364M, chain A/B/C/D, )
16: VAR_017086 (R374W, chain A/B/C/D, )
17: VAR_007977 (S395R, chain A/B/C/D, )
18: VAR_017087 (R396C, chain A/B/C/D, )
19: VAR_017088 (R396H, chain A/B/C/D, )
20: VAR_017089 (D422Y, chain A/B/C/D, )
21: VAR_017090 (L423V, chain A/B/C/D, )
22: VAR_007978 (R426H, chain A/B/C/D, )
23: VAR_017091 (D430N, chain A/B/C/D, )
24: VAR_000680 (S438P, chain A/B/C/D, )
25: VAR_017092 (S447P, chain A/B/C/D, )
26: VAR_016932 (T450S, chain A/B/C/D, )
27: VAR_017093 (R452P, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_016931
M
26
L
PUR8_HUMAN
Disease (ADSL deficiency)
---
A/B/C/D
M
26
L
02
UniProt
VAR_037883
S
31
N
PUR8_HUMAN
Polymorphism
5757921
A/B/C/D
S
31
N
03
UniProt
VAR_007972
I
72
V
PUR8_HUMAN
Disease (ADSL deficiency)
---
A/B/C/D
I
72
V
04
UniProt
VAR_017079
P
100
A
PUR8_HUMAN
Disease (ADSL deficiency)
---
A/B/C/D
P
100
A
05
UniProt
VAR_017080
Y
114
H
PUR8_HUMAN
Disease (ADSL deficiency)
---
A/B/C/D
Y
114
H
06
UniProt
VAR_007973
R
141
W
PUR8_HUMAN
Disease (ADSL deficiency)
---
A/B/C/D
R
141
W
07
UniProt
VAR_037884
K
147
M
PUR8_HUMAN
Polymorphism
11089991
A/B/C/D
K
147
M
08
UniProt
VAR_007974
R
190
Q
PUR8_HUMAN
Disease (ADSL deficiency)
28941471
A/B/C/D
R
190
Q
09
UniProt
VAR_017081
R
194
C
PUR8_HUMAN
Disease (ADSL deficiency)
---
A/B/C/D
R
194
C
10
UniProt
VAR_007975
K
246
E
PUR8_HUMAN
Disease (ADSL deficiency)
---
A/B/C/D
K
246
E
11
UniProt
VAR_017082
D
268
N
PUR8_HUMAN
Disease (ADSL deficiency)
---
A/B/C/D
D
268
N
12
UniProt
VAR_007976
R
303
C
PUR8_HUMAN
Disease (ADSL deficiency)
---
A/B/C/D
R
303
C
13
UniProt
VAR_017083
L
311
V
PUR8_HUMAN
Disease (ADSL deficiency)
---
A/B/C/D
L
311
V
14
UniProt
VAR_017084
P
318
L
PUR8_HUMAN
Disease (ADSL deficiency)
---
A/B/C/D
P
318
L
15
UniProt
VAR_017085
V
364
M
PUR8_HUMAN
Disease (ADSL deficiency)
---
A/B/C/D
V
364
M
16
UniProt
VAR_017086
R
374
W
PUR8_HUMAN
Disease (ADSL deficiency)
---
A/B/C/D
R
374
W
17
UniProt
VAR_007977
S
395
R
PUR8_HUMAN
Disease (ADSL deficiency)
---
A/B/C/D
S
395
R
18
UniProt
VAR_017087
R
396
C
PUR8_HUMAN
Disease (ADSL deficiency)
---
A/B/C/D
R
396
C
19
UniProt
VAR_017088
R
396
H
PUR8_HUMAN
Disease (ADSL deficiency)
---
A/B/C/D
R
396
H
20
UniProt
VAR_017089
D
422
Y
PUR8_HUMAN
Disease (ADSL deficiency)
---
A/B/C/D
D
422
Y
21
UniProt
VAR_017090
L
423
V
PUR8_HUMAN
Disease (ADSL deficiency)
---
A/B/C/D
L
423
V
22
UniProt
VAR_007978
R
426
H
PUR8_HUMAN
Disease (ADSL deficiency)
---
A/B/C/D
R
426
H
23
UniProt
VAR_017091
D
430
N
PUR8_HUMAN
Disease (ADSL deficiency)
---
A/B/C/D
D
430
N
24
UniProt
VAR_000680
S
438
P
PUR8_HUMAN
Disease (ADSL deficiency)
---
A/B/C/D
S
438
P
25
UniProt
VAR_017092
S
447
P
PUR8_HUMAN
Disease (ADSL deficiency)
---
A/B/C/D
S
447
P
26
UniProt
VAR_016932
T
450
S
PUR8_HUMAN
Disease (ADSL deficiency)
---
A/B/C/D
T
450
S
27
UniProt
VAR_017093
R
452
P
PUR8_HUMAN
Disease (ADSL deficiency)
---
A/B/C/D
R
452
P
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: FUMARATE_LYASES (A:293-297,B:294-297,C:294-297,D:29...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FUMARATE_LYASES
PS00163
Fumarate lyases signature.
PUR8_HUMAN
288-297
4
A:293-297
B:294-297
C:294-297
D:293-297
[
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]
Exons
(0, 0)
Info
All Exons
View:
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All Exon Boundaries
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Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_ADSL_C_2vd6D01 (D:377-461)
1b: PFAM_ADSL_C_2vd6D02 (D:377-461)
1c: PFAM_ADSL_C_2vd6D03 (D:377-461)
1d: PFAM_ADSL_C_2vd6D04 (D:377-461)
2a: PFAM_Lyase_1_2vd6D05 (D:28-313)
2b: PFAM_Lyase_1_2vd6D06 (D:28-313)
2c: PFAM_Lyase_1_2vd6D07 (D:28-313)
2d: PFAM_Lyase_1_2vd6D08 (D:28-313)
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Clans
(
)
(
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Families
(
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(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: ADSL_C]
(6)
Family
:
ADSL_C
(6)
Homo sapiens (Human)
(1)
1a
ADSL_C-2vd6D01
D:377-461
1b
ADSL_C-2vd6D02
D:377-461
1c
ADSL_C-2vd6D03
D:377-461
1d
ADSL_C-2vd6D04
D:377-461
Clan
:
no clan defined [family: Lyase_1]
(27)
Family
:
Lyase_1
(27)
Homo sapiens (Human)
(2)
2a
Lyase_1-2vd6D05
D:28-313
2b
Lyase_1-2vd6D06
D:28-313
2c
Lyase_1-2vd6D07
D:28-313
2d
Lyase_1-2vd6D08
D:28-313
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