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1D6N
Biol. Unit 1
Info
Asym.Unit (71 KB)
Biol.Unit 1 (64 KB)
Biol.Unit 2 (126 KB)
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(1)
Title
:
TERNARY COMPLEX STRUCTURE OF HUMAN HGPRTASE, PRPP, MG2+, AND THE INHIBITOR HPP REVEALS THE INVOLVEMENT OF THE FLEXIBLE LOOP IN SUBSTRATE BINDING
Authors
:
G. K. Balendiran
Date
:
14 Oct 99 (Deposition) - 30 Dec 99 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Biol. Unit 2: A,B (2x)
Keywords
:
Hgprtase, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. K. Balendiran, J. A. Molina, Y. Xu, J. Torres-Martinez, R. Stevens, P. J. Focia, A. E. Eakin, J. C. Sacchettini, S. P. Craig 3Rd.
Ternary Complex Structure Of Human Hgprtase, Prpp, Mg2+, And The Inhibitor Hpp Reveals The Involvement Of The Flexible Loop In Substrate Binding.
Protein Sci. V. 8 1023 1999
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 4)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
2a: 3H-PYRAZOLO[4,3-D]PYRIMIDIN-7-OL (PPOa)
2b: 3H-PYRAZOLO[4,3-D]PYRIMIDIN-7-OL (PPOb)
3a: ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC... (PRPa)
3b: ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC... (PRPb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
-1
Ligand/Ion
MAGNESIUM ION
2
PPO
2
Ligand/Ion
3H-PYRAZOLO[4,3-D]PYRIMIDIN-7-OL
3
PRP
2
Ligand/Ion
ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID
[
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
GLU A:133 , ASP A:134 , PRP A:312 , HOH A:989 , HOH A:990
BINDING SITE FOR RESIDUE MG A 313
2
AC2
SOFTWARE
VAL B:66 , GLU B:133 , ASP B:134 , PRP B:314 , HOH B:991 , HOH B:992
BINDING SITE FOR RESIDUE MG B 315
3
AC3
SOFTWARE
ILE A:135 , ASP A:137 , LYS A:165 , LYS A:185 , PHE A:186 , VAL A:187 , ASP A:193
BINDING SITE FOR RESIDUE PPO A 300
4
AC4
SOFTWARE
LEU A:67 , ALA A:68 , GLY A:69 , GLY A:70 , SER A:103 , TYR A:104 , GLU A:133 , ASP A:134 , ILE A:135 , ASP A:137 , THR A:138 , GLY A:139 , LYS A:140 , THR A:141 , MG A:313 , HOH A:989 , HOH A:990
BINDING SITE FOR RESIDUE PRP A 312
5
AC5
SOFTWARE
TYR B:104 , ILE B:135 , LYS B:165 , PHE B:186 , VAL B:187 , ASP B:193 , PRP B:314
BINDING SITE FOR RESIDUE PPO B 301
6
AC6
SOFTWARE
GLY B:69 , SER B:103 , TYR B:104 , CYS B:105 , GLU B:133 , ASP B:134 , ASP B:137 , THR B:138 , GLY B:139 , LYS B:140 , THR B:141 , LEU B:192 , ASP B:193 , PPO B:301 , MG B:315 , HOH B:992
BINDING SITE FOR RESIDUE PRP B 314
[
close Site info
]
SAPs(SNPs)/Variants
(65, 130)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_006750 (G6D, chain A/B, )
02: VAR_006751 (V7G, chain A/B, )
03: VAR_006752 (G15D, chain A/B, )
04: VAR_006753 (G15S, chain A/B, )
05: VAR_006754 (D19V, chain A/B, )
06: VAR_071610 (C22F, chain A/B, )
07: VAR_006755 (C22W, chain A/B, )
08: VAR_006756 (L40P, chain A/B, )
09: VAR_006757 (I41F, chain A/B, )
10: VAR_006758 (I41T, chain A/B, )
11: VAR_071611 (D43Y, chain A/B, )
12: VAR_006760 (R44K, chain A/B, )
13: VAR_006761 (R47H, chain A/B, )
14: VAR_006763 (A49P, chain A/B, )
15: VAR_006762 (A49V, chain A/B, )
16: VAR_006764 (R50G, chain A/B, )
17: VAR_006765 (R50P, chain A/B, )
18: VAR_006766 (D51G, chain A/B, )
19: VAR_006767 (V52A, chain A/B, )
20: VAR_006768 (V52M, chain A/B, )
21: VAR_006769 (M53L, chain A/B, )
22: VAR_006770 (M56T, chain A/B, )
23: VAR_006771 (G57R, chain A/B, )
24: VAR_071612 (H59R, chain A/B, )
25: VAR_006772 (H60R, chain A/B, )
26: VAR_071613 (A63P, chain A/B, )
27: VAR_071614 (L64P, chain A/B, )
28: VAR_006773 (G69E, chain A/B, )
29: VAR_006774 (G70R, chain A/B, )
30: VAR_071615 (Y71C, chain A/B, )
31: VAR_006775 (F73L, chain A/B, )
32: VAR_071616 (L77Q, chain A/B, )
33: VAR_006776 (L77V, chain A/B, )
34: VAR_006777 (D79V, chain A/B, )
35: VAR_006778 (S103R, chain A/B, )
36: VAR_006779 (S109L, chain A/B, )
37: VAR_071618 (T123P, chain A/B, )
38: VAR_006780 (V129D, chain A/B, )
39: VAR_006781 (L130S, chain A/B, )
40: VAR_006782 (I131M, chain A/B, )
41: VAR_006783 (I131T, chain A/B, )
42: VAR_006784 (D134G, chain A/B, )
43: VAR_006785 (M142K, chain A/B, )
44: VAR_071619 (L146P, chain A/B, )
45: VAR_071620 (K158E, chain A/B, )
46: VAR_006787 (A160S, chain A/B, )
47: VAR_006788 (S161R, chain A/B, )
48: VAR_006789 (T167I, chain A/B, )
49: VAR_006790 (P175L, chain A/B, )
50: VAR_006791 (D176V, chain A/B, )
51: VAR_006792 (D176Y, chain A/B, )
52: VAR_006796 (I182T, chain A/B, )
53: VAR_071622 (D184G, chain A/B, )
54: VAR_006795 (V187A, chain A/B, )
55: VAR_071623 (A191V, chain A/B, )
56: VAR_006797 (D193E, chain A/B, )
57: VAR_006798 (D193N, chain A/B, )
58: VAR_006799 (Y194C, chain A/B, )
59: VAR_006800 (F198V, chain A/B, )
60: VAR_006801 (D200G, chain A/B, )
61: VAR_006802 (D200N, chain A/B, )
62: VAR_006803 (D200Y, chain A/B, )
63: VAR_006804 (H203D, chain A/B, )
64: VAR_006805 (H203R, chain A/B, )
65: VAR_006806 (C205Y, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_006750
G
7
D
HPRT_HUMAN
Disease (GOUT-HPRT)
---
A/B
G
6
D
02
UniProt
VAR_006751
V
8
G
HPRT_HUMAN
Disease (LNS)
---
A/B
V
7
G
03
UniProt
VAR_006752
G
16
D
HPRT_HUMAN
Disease (LNS)
---
A/B
G
15
D
04
UniProt
VAR_006753
G
16
S
HPRT_HUMAN
Disease (GOUT-HPRT)
---
A/B
G
15
S
05
UniProt
VAR_006754
D
20
V
HPRT_HUMAN
Disease (GOUT-HPRT)
---
A/B
D
19
V
06
UniProt
VAR_071610
C
23
F
HPRT_HUMAN
Disease (GOUT-HPRT)
---
A/B
C
22
F
07
UniProt
VAR_006755
C
23
W
HPRT_HUMAN
Disease (GOUT-HPRT)
---
A/B
C
22
W
08
UniProt
VAR_006756
L
41
P
HPRT_HUMAN
Disease (LNS)
---
A/B
L
40
P
09
UniProt
VAR_006757
I
42
F
HPRT_HUMAN
Disease (LNS)
---
A/B
I
41
F
10
UniProt
VAR_006758
I
42
T
HPRT_HUMAN
Disease (LNS)
---
A/B
I
41
T
11
UniProt
VAR_071611
D
44
Y
HPRT_HUMAN
Disease (LNS)
---
A/B
D
43
Y
12
UniProt
VAR_006760
R
45
K
HPRT_HUMAN
Disease (LNS)
---
A/B
R
44
K
13
UniProt
VAR_006761
R
48
H
HPRT_HUMAN
Disease (GOUT-HPRT)
---
A/B
R
47
H
14
UniProt
VAR_006763
A
50
P
HPRT_HUMAN
Disease (LNS)
---
A/B
A
49
P
15
UniProt
VAR_006762
A
50
V
HPRT_HUMAN
Disease (LNS)
---
A/B
A
49
V
16
UniProt
VAR_006764
R
51
G
HPRT_HUMAN
Disease (GOUT-HPRT)
---
A/B
R
50
G
17
UniProt
VAR_006765
R
51
P
HPRT_HUMAN
Disease (LNS)
---
A/B
R
50
P
18
UniProt
VAR_006766
D
52
G
HPRT_HUMAN
Unclassified
---
A/B
D
51
G
19
UniProt
VAR_006767
V
53
A
HPRT_HUMAN
Disease (GOUT-HPRT)
---
A/B
V
52
A
20
UniProt
VAR_006768
V
53
M
HPRT_HUMAN
Disease (GOUT-HPRT)
---
A/B
V
52
M
21
UniProt
VAR_006769
M
54
L
HPRT_HUMAN
Disease (LNS)
---
A/B
M
53
L
22
UniProt
VAR_006770
M
57
T
HPRT_HUMAN
Disease (LNS)
---
A/B
M
56
T
23
UniProt
VAR_006771
G
58
R
HPRT_HUMAN
Disease (GOUT-HPRT)
---
A/B
G
57
R
24
UniProt
VAR_071612
H
60
R
HPRT_HUMAN
Disease (GOUT-HPRT)
---
A/B
H
59
R
25
UniProt
VAR_006772
H
61
R
HPRT_HUMAN
Unclassified
---
A/B
H
60
R
26
UniProt
VAR_071613
A
64
P
HPRT_HUMAN
Disease (LNS)
---
A/B
A
63
P
27
UniProt
VAR_071614
L
65
P
HPRT_HUMAN
Disease (LNS)
---
A/B
L
64
P
28
UniProt
VAR_006773
G
70
E
HPRT_HUMAN
Disease (LNS)
---
A/B
G
69
E
29
UniProt
VAR_006774
G
71
R
HPRT_HUMAN
Disease (LNS)
---
A/B
G
70
R
30
UniProt
VAR_071615
Y
72
C
HPRT_HUMAN
Disease (LNS)
---
A/B
Y
71
C
31
UniProt
VAR_006775
F
74
L
HPRT_HUMAN
Disease (LNS)
---
A/B
F
73
L
32
UniProt
VAR_071616
L
78
Q
HPRT_HUMAN
Disease (LNS)
---
A/B
L
77
Q
33
UniProt
VAR_006776
L
78
V
HPRT_HUMAN
Disease (GOUT-HPRT)
---
A/B
L
77
V
34
UniProt
VAR_006777
D
80
V
HPRT_HUMAN
Disease (GOUT-HPRT)
---
A/B
D
79
V
35
UniProt
VAR_006778
S
104
R
HPRT_HUMAN
Disease (GOUT-HPRT)
---
A/B
S
103
R
36
UniProt
VAR_006779
S
110
L
HPRT_HUMAN
Disease (GOUT-HPRT)
---
A/B
S
109
L
37
UniProt
VAR_071618
T
124
P
HPRT_HUMAN
Disease (GOUT-HPRT)
---
A/B
T
123
P
38
UniProt
VAR_006780
V
130
D
HPRT_HUMAN
Disease (LNS)
---
A/B
V
129
D
39
UniProt
VAR_006781
L
131
S
HPRT_HUMAN
Disease (LNS)
---
A/B
L
130
S
40
UniProt
VAR_006782
I
132
M
HPRT_HUMAN
Disease (GOUT-HPRT)
---
A/B
I
131
M
41
UniProt
VAR_006783
I
132
T
HPRT_HUMAN
Disease (LNS)
---
A/B
I
131
T
42
UniProt
VAR_006784
D
135
G
HPRT_HUMAN
Disease (GOUT-HPRT)
---
A/B
D
134
G
43
UniProt
VAR_006785
M
143
K
HPRT_HUMAN
Disease (LNS)
---
A/B
M
142
K
44
UniProt
VAR_071619
L
147
P
HPRT_HUMAN
Disease (LNS)
---
A/B
L
146
P
45
UniProt
VAR_071620
K
159
E
HPRT_HUMAN
Disease (LNS)
---
A/B
K
158
E
46
UniProt
VAR_006787
A
161
S
HPRT_HUMAN
Disease (GOUT-HPRT)
---
A/B
A
160
S
47
UniProt
VAR_006788
S
162
R
HPRT_HUMAN
Disease (LNS)
---
A/B
S
161
R
48
UniProt
VAR_006789
T
168
I
HPRT_HUMAN
Disease (GOUT-HPRT)
---
A/B
T
167
I
49
UniProt
VAR_006790
P
176
L
HPRT_HUMAN
Disease (LNS)
---
A/B
P
175
L
50
UniProt
VAR_006791
D
177
V
HPRT_HUMAN
Disease (LNS)
---
A/B
D
176
V
51
UniProt
VAR_006792
D
177
Y
HPRT_HUMAN
Disease (LNS)
---
A/B
D
176
Y
52
UniProt
VAR_006796
I
183
T
HPRT_HUMAN
Disease (GOUT-HPRT)
---
A/B
I
182
T
53
UniProt
VAR_071622
D
185
G
HPRT_HUMAN
Disease (GOUT-HPRT)
---
A/B
D
184
G
54
UniProt
VAR_006795
V
188
A
HPRT_HUMAN
Unclassified
---
A/B
V
187
A
55
UniProt
VAR_071623
A
192
V
HPRT_HUMAN
Disease (GOUT-HPRT)
---
A/B
A
191
V
56
UniProt
VAR_006797
D
194
E
HPRT_HUMAN
Disease (GOUT-HPRT)
---
A/B
D
193
E
57
UniProt
VAR_006798
D
194
N
HPRT_HUMAN
Disease (LNS)
---
A/B
D
193
N
58
UniProt
VAR_006799
Y
195
C
HPRT_HUMAN
Disease (GOUT-HPRT)
---
A/B
Y
194
C
59
UniProt
VAR_006800
F
199
V
HPRT_HUMAN
Disease (LNS)
---
A/B
F
198
V
60
UniProt
VAR_006801
D
201
G
HPRT_HUMAN
Disease (GOUT-HPRT)
---
A/B
D
200
G
61
UniProt
VAR_006802
D
201
N
HPRT_HUMAN
Disease (GOUT-HPRT)
---
A/B
D
200
N
62
UniProt
VAR_006803
D
201
Y
HPRT_HUMAN
Disease (LNS)
---
A/B
D
200
Y
63
UniProt
VAR_006804
H
204
D
HPRT_HUMAN
Disease (LNS)
---
A/B
H
203
D
64
UniProt
VAR_006805
H
204
R
HPRT_HUMAN
Disease (LNS)
---
A/B
H
203
R
65
UniProt
VAR_006806
C
206
Y
HPRT_HUMAN
Disease (LNS)
---
A/B
C
205
Y
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: PUR_PYR_PR_TRANSFER (A:129-141,B:129-141)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PUR_PYR_PR_TRANSFER
PS00103
Purine/pyrimidine phosphoribosyl transferases signature.
HPRT_HUMAN
130-142
2
A:129-141
B:129-141
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
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
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1d6na_ (A:)
1b: SCOP_d1d6nb_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
PRTase-like
(145)
Superfamily
:
PRTase-like
(145)
Family
:
Phosphoribosyltransferases (PRTases)
(100)
Protein domain
:
Hypoxanthine-guanine PRTase (HGPRTase)
(11)
Human (Homo sapiens) [TaxId: 9606]
(9)
1a
d1d6na_
A:
1b
d1d6nb_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1d6nA00 (A:4-217)
1b: CATH_1d6nB00 (B:4-217)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
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
1d6nA00
A:4-217
1b
1d6nB00
B:4-217
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
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Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
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Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
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