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2H08
Asym. Unit
Info
Asym.Unit (104 KB)
Biol.Unit 1 (292 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE 1 MUTANT Y146M
Authors
:
S. Li, B. Peng, J. Ding
Date
:
14 May 06 (Deposition) - 24 Oct 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (3x)
Keywords
:
Prs1, Prpp Synthetase 1, Phosphoribosyl Pyrophosphate Synthetase 1, Mutant, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Li, Y. Lu, B. Peng, J. Ding
Crystal Structure Of Human Phosphoribosylpyrophosphate Synthetase 1 Reveals A Novel Allosteric Site
Biochem. J. V. 401 39 2007
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Hetero Components
(1, 6)
Info
All Hetero Components
1a: SULFATE ION (SO4a)
1b: SULFATE ION (SO4b)
1c: SULFATE ION (SO4c)
1d: SULFATE ION (SO4d)
1e: SULFATE ION (SO4e)
1f: SULFATE ION (SO4f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
SO4
6
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP B:224 , THR B:225 , CYS B:226 , GLY B:227 , THR B:228 , HOH B:1061
BINDING SITE FOR RESIDUE SO4 B 1001
2
AC2
SOFTWARE
ASP A:224 , THR A:225 , CYS A:226 , GLY A:227 , THR A:228 , HOH A:1072 , HOH A:1074
BINDING SITE FOR RESIDUE SO4 A 1002
3
AC3
SOFTWARE
ARG A:104 , SER B:47 , ARG B:49 , SER B:308 , VAL B:309 , SER B:310 , HOH B:1045
BINDING SITE FOR RESIDUE SO4 B 1003
4
AC4
SOFTWARE
SER A:47 , ARG A:49 , SER A:308 , VAL A:309 , SER A:310 , HOH A:1014 , HOH A:1034 , ARG B:104
BINDING SITE FOR RESIDUE SO4 A 1004
5
AC5
SOFTWARE
LYS A:100 , ASP A:101 , LYS A:102 , SER B:132 , GLN B:135 , ASN B:144 , HOH B:1007 , HOH B:1082
BINDING SITE FOR RESIDUE SO4 B 1005
6
AC6
SOFTWARE
SER A:132 , GLN A:135 , ASN A:144 , HOH A:1020 , HOH A:1079 , LYS B:100 , ASP B:101 , LYS B:102
BINDING SITE FOR RESIDUE SO4 A 1006
[
close Site info
]
SAPs(SNPs)/Variants
(18, 36)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_072719 (S16P, chain A/B, )
02: VAR_036941 (E43D, chain A/B, )
03: VAR_016044 (D52H, chain A/B, )
04: VAR_063522 (D65N, chain A/B, )
05: VAR_063523 (A87T, chain A/B, )
06: VAR_004163 (N114S, chain A/B, )
07: VAR_036942 (M115T, chain A/B, )
08: VAR_016045 (L129I, chain A/B, )
09: VAR_036943 (Q133P, chain A/B, )
10: VAR_036944 (L152P, chain A/B, )
11: VAR_004164 (D183H, chain A/B, )
12: VAR_016046 (A190V, chain A/B, )
13: VAR_016047 (H193Q, chain A/B, )
14: VAR_036593 (D203H, chain A/B, )
15: VAR_036594 (V219G, chain A/B, )
16: VAR_036595 (H231D, chain A/B, )
17: VAR_063524 (I290T, chain A/B, )
18: VAR_063525 (G306R, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_072719
S
16
P
PRPS1_HUMAN
Disease
---
A/B
S
16
P
02
UniProt
VAR_036941
E
43
D
PRPS1_HUMAN
Disease (CMTX5)
---
A/B
E
43
D
03
UniProt
VAR_016044
D
52
H
PRPS1_HUMAN
Disease (PRPS1 superactivity)
---
A/B
D
52
H
04
UniProt
VAR_063522
D
65
N
PRPS1_HUMAN
Disease (DFNX1)
---
A/B
D
65
N
05
UniProt
VAR_063523
A
87
T
PRPS1_HUMAN
Disease (DFNX1)
---
A/B
A
87
T
06
UniProt
VAR_004163
N
114
S
PRPS1_HUMAN
Disease (PRPS1 superactivity)
---
A/B
N
114
S
07
UniProt
VAR_036942
M
115
T
PRPS1_HUMAN
Disease (CMTX5)
---
A/B
M
115
T
08
UniProt
VAR_016045
L
129
I
PRPS1_HUMAN
Disease (PRPS1 superactivity)
---
A/B
L
129
I
09
UniProt
VAR_036943
Q
133
P
PRPS1_HUMAN
Disease (ARTS)
---
A/B
Q
133
P
10
UniProt
VAR_036944
L
152
P
PRPS1_HUMAN
Disease (ARTS)
---
A/B
L
152
P
11
UniProt
VAR_004164
D
183
H
PRPS1_HUMAN
Disease (PRPS1 superactivity)
---
A/B
D
183
H
12
UniProt
VAR_016046
A
190
V
PRPS1_HUMAN
Disease (PRPS1 superactivity)
---
A/B
A
190
V
13
UniProt
VAR_016047
H
193
Q
PRPS1_HUMAN
Disease (PRPS1 superactivity)
---
A/B
H
193
Q
14
UniProt
VAR_036593
D
203
H
PRPS1_HUMAN
Unclassified
---
A/B
D
203
H
15
UniProt
VAR_036594
V
219
G
PRPS1_HUMAN
Unclassified
---
A/B
V
219
G
16
UniProt
VAR_036595
H
231
D
PRPS1_HUMAN
Unclassified
---
A/B
H
231
D
17
UniProt
VAR_063524
I
290
T
PRPS1_HUMAN
Disease (DFNX1)
---
A/B
I
290
T
18
UniProt
VAR_063525
G
306
R
PRPS1_HUMAN
Disease (DFNX1)
---
A/B
G
306
R
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: PRPP_SYNTHASE (A:128-143,B:128-143)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PRPP_SYNTHASE
PS00114
Phosphoribosyl pyrophosphate synthase signature.
PRPS1_HUMAN
128-143
2
A:128-143
B:128-143
[
close PROSITE info
]
Exons
(7, 14)
Info
All Exons
Exon 1.1b (A:3-41 | B:3-41)
Exon 1.2a (A:41-102 | B:41-102)
Exon 1.3a (A:103-135 | B:103-135)
Exon 1.4 (A:136-177 | B:136-177)
Exon 1.5 (A:177-235 (gaps) | B:177-235 (gaps...)
Exon 1.6 (A:235-288 | B:235-288)
Exon 1.7b (A:289-313 | B:289-317)
View:
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All Exon Boundaries
1: Boundary -/1.1b
2: Boundary 1.1b/1.2a
3: Boundary 1.2a/1.3a
4: Boundary 1.3a/1.4
5: Boundary 1.4/1.5
6: Boundary 1.5/1.6
7: Boundary 1.6/1.7b
8: Boundary 1.7b/-
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
1.1b
ENST00000372435
1b
ENSE00001947916
X:106871737-106871980
244
PRPS1_HUMAN
1-41
41
2
A:3-41
B:3-41
39
39
1.2a
ENST00000372435
2a
ENSE00001708019
X:106882525-106882708
184
PRPS1_HUMAN
41-102
62
2
A:41-102
B:41-102
62
62
1.3a
ENST00000372435
3a
ENSE00001668533
X:106884132-106884230
99
PRPS1_HUMAN
103-135
33
2
A:103-135
B:103-135
33
33
1.4
ENST00000372435
4
ENSE00001201231
X:106885596-106885720
125
PRPS1_HUMAN
136-177
42
2
A:136-177
B:136-177
42
42
1.5
ENST00000372435
5
ENSE00001201225
X:106888407-106888580
174
PRPS1_HUMAN
177-235
59
2
A:177-235 (gaps)
B:177-235 (gaps)
59
59
1.6
ENST00000372435
6
ENSE00001201218
X:106890836-106890995
160
PRPS1_HUMAN
235-288
54
2
A:235-288
B:235-288
54
54
1.7b
ENST00000372435
7b
ENSE00001457786
X:106893170-106894256
1087
PRPS1_HUMAN
289-318
30
2
A:289-313
B:289-317
25
29
[
close EXON info
]
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2h08a1 (A:3-160)
1b: SCOP_d2h08a2 (A:161-313)
1c: SCOP_d2h08b1 (B:3-160)
1d: SCOP_d2h08b2 (B:161-317)
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(
)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
PRTase-like
(145)
Superfamily
:
PRTase-like
(145)
Family
:
automated matches
(39)
Protein domain
:
automated matches
(39)
Human (Homo sapiens) [TaxId: 9606]
(9)
1a
d2h08a1
A:3-160
1b
d2h08a2
A:161-313
1c
d2h08b1
B:3-160
1d
d2h08b2
B:161-317
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2h08A01 (A:3-146,A:291-311)
1b: CATH_2h08B01 (B:3-146,B:291-311)
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(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.2020, no name defined]
(117)
Human (Homo sapiens)
(19)
1a
2h08A01
A:3-146,A:291-311
1b
2h08B01
B:3-146,B:291-311
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
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