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3I2B
Biol. Unit 1
Info
Asym.Unit (272 KB)
Biol.Unit 1 (70 KB)
Biol.Unit 2 (71 KB)
Biol.Unit 3 (68 KB)
Biol.Unit 4 (69 KB)
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(1)
Title
:
THE CRYSTAL STRUCTURE OF HUMAN 6 PYRUVOYL TETRAHYDROBIOPTERIN SYNTHASE
Authors
:
E. Ugochukwu, R. Cocking, E. Pilka, W. W. Yue, J. E. Bray, A. Chaikuad, T. J. Muniz, F. Von Delft, C. Bountra, C. H. Arrowsmith, J. Weigelt, A. Ed U. Oppermann, Structural Genomics Consortium (Sgc)
Date
:
29 Jun 09 (Deposition) - 28 Jul 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,D,E (1x)
Biol. Unit 2: B,C,F (1x)
Biol. Unit 3: G,H,I (1x)
Biol. Unit 4: J,K,L (1x)
Keywords
:
6 Pyruvoyl Tetrahydrobiopterin Synthase, Pts, Ptp Synthase, Structural Genomics, Structural Genomics Consortium, Sgc, Disease Mutation, Lyase, Metal-Binding, Phenylketonuria, Phosphoprotein, Tetrahydrobiopterin Biosynthesis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Ugochukwu, R. Cocking, E. Pilka, W. W. Yue, J. E. Bray, A. Chaikuad, T. Krojer, J. Muniz, U. Oppermann
The Crystal Structure Of Human 6 Pyruvoyl Tetrahydrobiopterin Synthase
To Be Published
[
close entry info
]
Hetero Components
(1, 1)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
3a: NICKEL (II) ION (NIa)
3b: NICKEL (II) ION (NIb)
3c: NICKEL (II) ION (NIc)
3d: NICKEL (II) ION (NId)
3e: NICKEL (II) ION (NIe)
3f: NICKEL (II) ION (NIf)
3g: NICKEL (II) ION (NIg)
3h: NICKEL (II) ION (NIh)
3i: NICKEL (II) ION (NIi)
3j: NICKEL (II) ION (NIj)
3k: NICKEL (II) ION (NIk)
3l: NICKEL (II) ION (NIl)
4a: DI(HYDROXYETHYL)ETHER (PEGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
1
Ligand/Ion
1,2-ETHANEDIOL
2
MG
-1
Ligand/Ion
MAGNESIUM ION
3
NI
-1
Ligand/Ion
NICKEL (II) ION
4
PEG
-1
Ligand/Ion
DI(HYDROXYETHYL)ETHER
[
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]
Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: BC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:75 , GLU C:35
BINDING SITE FOR RESIDUE EDO A 1
2
AC2
SOFTWARE
HIS A:24 , HIS A:49 , HIS A:51 , GLU A:134 , HOH A:293
BINDING SITE FOR RESIDUE NI A 146
3
AC3
SOFTWARE
ASP A:116 , TYR A:142
BINDING SITE FOR RESIDUE MG A 2
4
AC4
SOFTWARE
HIS D:24 , HIS D:49 , HIS D:51 , GLU D:134 , HOH D:154
BINDING SITE FOR RESIDUE NI D 4
5
AC5
SOFTWARE
HIS E:24 , HIS E:49 , HIS E:51 , GLU E:134 , HOH E:152 , HOH E:277
BINDING SITE FOR RESIDUE NI E 146
6
AC6
SOFTWARE
GLU A:62 , ASP A:64 , GLU B:62 , ASP B:64 , VAL B:70
BINDING SITE FOR RESIDUE PEG B 1
7
BC2
SOFTWARE
HOH E:196 , HIS H:24 , HIS H:49 , HIS H:51 , GLU H:134 , HOH H:152
BINDING SITE FOR RESIDUE NI H 146
[
close Site info
]
SAPs(SNPs)/Variants
(24, 72)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_006816 (R16C, chain A/D/E, )
02: VAR_006817 (R25G, chain A/D/E, )
03: VAR_006818 (R25Q, chain A/D/E, )
04: VAR_058265 (L26F, chain A/D/E, )
05: VAR_006819 (E35G, chain A/D/E, )
06: VAR_006820 (N36K, chain A/D/E, )
07: VAR_008040 (N47D, chain A/D/E, )
08: VAR_006821 (N52S, chain A/D/E, )
09: VAR_006822 (V56M, chain A/D/E, )
10: VAR_006824 (T67M, chain A/D/E, )
11: VAR_006825 (V70D, chain A/D/E, )
12: VAR_006826 (P87L, chain A/D/E, )
13: VAR_006827 (P87S, chain A/D/E, )
14: VAR_006828 (D96N, chain A/D/E, )
15: VAR_058266 (V97M, chain A/D/E, )
16: VAR_058267 (Y99C, chain A/D/E, )
17: VAR_006829 (F100V, chain A/D/E, )
18: VAR_006830 (T106M, chain A/D/E, )
19: VAR_006831 (I114V, chain A/D/E, )
20: VAR_008041 (D116G, chain A/D/E, )
21: VAR_058268 (V124L, chain A/D/E, )
22: VAR_006832 (K129E, chain A/D/E, )
23: VAR_058269 (D136G, chain A/D/E, )
24: VAR_006833 (D136V, chain A/D/E, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_006816
R
16
C
PTPS_HUMAN
Disease (HPABH4A)
---
A/D/E
R
16
C
02
UniProt
VAR_006817
R
25
G
PTPS_HUMAN
Disease (HPABH4A)
---
A/D/E
R
25
G
03
UniProt
VAR_006818
R
25
Q
PTPS_HUMAN
Disease (HPABH4A)
---
A/D/E
R
25
Q
04
UniProt
VAR_058265
L
26
F
PTPS_HUMAN
Disease (HPABH4A)
---
A/D/E
L
26
F
05
UniProt
VAR_006819
E
35
G
PTPS_HUMAN
Disease (HPABH4A)
---
A/D/E
E
35
G
06
UniProt
VAR_006820
N
36
K
PTPS_HUMAN
Disease (HPABH4A)
---
A/D/E
N
36
K
07
UniProt
VAR_008040
N
47
D
PTPS_HUMAN
Disease (HPABH4A)
---
A/D/E
N
47
D
08
UniProt
VAR_006821
N
52
S
PTPS_HUMAN
Disease (HPABH4A)
---
A/D/E
N
52
S
09
UniProt
VAR_006822
V
56
M
PTPS_HUMAN
Disease (HPABH4A)
---
A/D/E
V
56
M
10
UniProt
VAR_006824
T
67
M
PTPS_HUMAN
Disease (HPABH4A)
---
A/D/E
T
67
M
11
UniProt
VAR_006825
V
70
D
PTPS_HUMAN
Disease (HPABH4A)
---
A/D/E
V
70
D
12
UniProt
VAR_006826
P
87
L
PTPS_HUMAN
Disease (HPABH4A)
---
A/D/E
P
87
L
13
UniProt
VAR_006827
P
87
S
PTPS_HUMAN
Disease (HPABH4A)
104894276
A/D/E
P
87
S
14
UniProt
VAR_006828
D
96
N
PTPS_HUMAN
Disease (HPABH4A)
104894280
A/D/E
D
96
N
15
UniProt
VAR_058266
V
97
M
PTPS_HUMAN
Disease (HPABH4A)
---
A/D/E
V
97
M
16
UniProt
VAR_058267
Y
99
C
PTPS_HUMAN
Disease (HPABH4A)
---
A/D/E
Y
99
C
17
UniProt
VAR_006829
F
100
V
PTPS_HUMAN
Disease (HPABH4A)
---
A/D/E
F
100
V
18
UniProt
VAR_006830
T
106
M
PTPS_HUMAN
Disease (HPABH4A)
---
A/D/E
T
106
M
19
UniProt
VAR_006831
I
114
V
PTPS_HUMAN
Disease (HPABH4A)
---
A/D/E
I
114
V
20
UniProt
VAR_008041
D
116
G
PTPS_HUMAN
Disease (HPABH4A)
---
A/D/E
D
116
G
21
UniProt
VAR_058268
V
124
L
PTPS_HUMAN
Disease (HPABH4A)
---
A/D/E
V
124
L
22
UniProt
VAR_006832
K
129
E
PTPS_HUMAN
Disease (HPABH4A)
---
A/D/E
K
129
E
23
UniProt
VAR_058269
D
136
G
PTPS_HUMAN
Disease (HPABH4A)
---
A/D/E
D
136
G
24
UniProt
VAR_006833
D
136
V
PTPS_HUMAN
Disease (HPABH4A)
---
A/D/E
D
136
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 6)
Info
All PROSITE Patterns/Profiles
1: PTPS_1 (A:43-53,D:43-53,E:43-53)
2: PTPS_2 (A:89-96,D:89-96,E:89-96)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PTPS_1
PS00987
6-pyruvoyl tetrahydropterin synthase signature 1.
PTPS_HUMAN
43-53
3
A:43-53
-
-
D:43-53
E:43-53
-
-
-
-
-
-
-
2
PTPS_2
PS00988
6-pyruvoyl tetrahydropterin synthase signature 2.
PTPS_HUMAN
89-96
3
A:89-96
-
-
D:89-96
E:89-96
-
-
-
-
-
-
-
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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, 12)
Info
All SCOP Domains
1a: SCOP_d3i2ba_ (A:)
1b: SCOP_d3i2bb_ (B:)
1c: SCOP_d3i2bk_ (K:)
1d: SCOP_d3i2bl_ (L:)
1e: SCOP_d3i2bc_ (C:)
1f: SCOP_d3i2bd_ (D:)
1g: SCOP_d3i2be_ (E:)
1h: SCOP_d3i2bf_ (F:)
1i: SCOP_d3i2bg_ (G:)
1j: SCOP_d3i2bh_ (H:)
1k: SCOP_d3i2bi_ (I:)
1l: SCOP_d3i2bj_ (J:)
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(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
T-fold
(116)
Superfamily
:
Tetrahydrobiopterin biosynthesis enzymes-like
(113)
Family
:
automated matches
(13)
Protein domain
:
automated matches
(13)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d3i2ba_
A:
1b
d3i2bb_
B:
1c
d3i2bk_
K:
1d
d3i2bl_
L:
1e
d3i2bc_
C:
1f
d3i2bd_
D:
1g
d3i2be_
E:
1h
d3i2bf_
F:
1i
d3i2bg_
G:
1j
d3i2bh_
H:
1k
d3i2bi_
I:
1l
d3i2bj_
J:
[
close SCOP info
]
CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_3i2bA00 (A:8-145)
1b: CATH_3i2bB00 (B:8-145)
1c: CATH_3i2bJ00 (J:9-145)
1d: CATH_3i2bG00 (G:10-145)
1e: CATH_3i2bD00 (D:8-145)
1f: CATH_3i2bE00 (E:8-145)
1g: CATH_3i2bF00 (F:8-145)
1h: CATH_3i2bI00 (I:8-145)
1i: CATH_3i2bK00 (K:8-145)
1j: CATH_3i2bL00 (L:8-145)
1k: CATH_3i2bC00 (C:9-145)
1l: CATH_3i2bH00 (H:9-145)
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Tetrahydropterin Synthase; Chain A
(11)
Homologous Superfamily
:
[code=3.30.479.10, no name defined]
(8)
Human (Homo sapiens)
(1)
1a
3i2bA00
A:8-145
1b
3i2bB00
B:8-145
1c
3i2bJ00
J:9-145
1d
3i2bG00
G:10-145
1e
3i2bD00
D:8-145
1f
3i2bE00
E:8-145
1g
3i2bF00
F:8-145
1h
3i2bI00
I:8-145
1i
3i2bK00
K:8-145
1j
3i2bL00
L:8-145
1k
3i2bC00
C:9-145
1l
3i2bH00
H:9-145
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Label:
Sorry, no Info available
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