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1PKX
Asym. Unit
Info
Asym.Unit (384 KB)
Biol.Unit 1 (193 KB)
Biol.Unit 2 (192 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN ATIC IN COMPLEX WITH XMP
Authors
:
D. W. Wolan, C. G. Cheong, S. E. Greasley, I. A. Wilson
Date
:
06 Jun 03 (Deposition) - 17 Feb 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Atic, Aicar Transformylase, Imp Cyclohydrolase, Xanthosine Monophosphate, Purine Biosynthesis, Transferase, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. W. Wolan, C. G. Cheong, S. E. Greasley, I. A. Wilson
Structural Insights Into The Human And Avian Imp Cyclohydrolase Mechanism Via Crystal Structures With The Bound Xmp Inhibitor.
Biochemistry V. 43 1171 2004
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 6)
Info
All Hetero Components
1a: POTASSIUM ION (Ka)
1b: POTASSIUM ION (Kb)
1c: POTASSIUM ION (Kc)
1d: POTASSIUM ION (Kd)
2a: XANTHOSINE-5'-MONOPHOSPHATE (XMPa)
2b: XANTHOSINE-5'-MONOPHOSPHATE (XMPb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
K
4
Ligand/Ion
POTASSIUM ION
2
XMP
2
Ligand/Ion
XANTHOSINE-5'-MONOPHOSPHATE
[
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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
VAL A:425 , THR A:428 , SER A:430 , SER A:432 , ASP A:539 , LEU A:589 , HIS A:591
BINDING SITE FOR RESIDUE K A 2001
2
AC2
SOFTWARE
VAL B:425 , THR B:428 , SER B:430 , SER B:432 , ASP B:539 , LEU B:589
BINDING SITE FOR RESIDUE K B 2002
3
AC3
SOFTWARE
VAL C:425 , THR C:428 , SER C:430 , SER C:432 , ASP C:539 , LEU C:589 , HIS C:591
BINDING SITE FOR RESIDUE K C 2003
4
AC4
SOFTWARE
VAL D:425 , THR D:428 , SER D:430 , SER D:432 , ASP D:539 , LEU D:589 , HIS D:591
BINDING SITE FOR RESIDUE K D 2004
5
AC5
SOFTWARE
SER A:10 , VAL A:11 , SER A:12 , LYS A:14 , SER A:34 , GLY A:36 , THR A:37 , ARG A:64 , LYS A:66 , THR A:67 , CYS A:101 , ASN A:102 , LEU A:103 , TYR A:104 , ASP A:125 , ILE A:126 , GLY A:127 , GLY A:128
BINDING SITE FOR RESIDUE XMP A 1901
6
AC6
SOFTWARE
SER C:10 , VAL C:11 , SER C:12 , LYS C:14 , SER C:34 , GLY C:36 , THR C:37 , ARG C:64 , LYS C:66 , THR C:67 , CYS C:101 , ASN C:102 , LEU C:103 , TYR C:104 , ASP C:125 , ILE C:126 , GLY C:127 , GLY C:128 , HOH C:2074
BINDING SITE FOR RESIDUE XMP C 1903
[
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SAPs(SNPs)/Variants
(2, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_019306 (T116S, chain A/B/C/D, )
2: VAR_019307 (K426R, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_019306
T
116
S
PUR9_HUMAN
Polymorphism
2372536
A/B/C/D
T
116
S
2
UniProt
VAR_019307
K
426
R
PUR9_HUMAN
Disease (AICAR)
---
A/B/C/D
K
426
R
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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]
Exons
(16, 64)
Info
All Exons
Exon 1.1a (A:3-7 | B:4-7 | C:4-7 | D:4-7)
Exon 1.1g (A:7-49 | B:7-49 | C:7-49 | D:7-49)
Exon 1.2b (A:49-75 | B:49-75 | C:49-75 | D:49...)
Exon 1.3 (A:75-97 | B:75-97 | C:75-97 | D:75...)
Exon 1.4b (A:97-127 | B:97-127 | C:97-127 | D...)
Exon 1.5b (A:127-177 | B:127-177 | C:127-177 ...)
Exon 1.6 (A:178-230 | B:178-230 | C:178-230 ...)
Exon 1.7 (A:230-272 | B:230-272 | C:230-272 ...)
Exon 1.8 (A:272-308 | B:272-308 | C:272-308 ...)
Exon 1.9b (A:308-336 | B:308-336 | C:308-336 ...)
Exon 1.10b (A:337-366 | B:337-366 | C:337-366 ...)
Exon 1.11c (A:367-409 | B:367-409 | C:367-409 ...)
Exon 1.12a (A:410-440 | B:410-440 | C:410-440 ...)
Exon 1.13a (A:441-501 (gaps) | B:441-501 | C:4...)
Exon 1.16b (A:502-553 | B:502-553 | C:502-553 ...)
Exon 1.17c (A:554-592 | B:554-592 | C:554-592 ...)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1a
02: Boundary 1.1a/1.1g
03: Boundary 1.1g/1.2b
04: Boundary 1.2b/1.3
05: Boundary 1.3/1.4b
06: Boundary 1.4b/1.5b
07: Boundary 1.5b/1.6
08: Boundary 1.6/1.7
09: Boundary 1.7/1.8
10: Boundary 1.8/1.9b
11: Boundary 1.9b/1.10b
12: Boundary 1.10b/1.11c
13: Boundary 1.11c/1.12a
14: Boundary 1.12a/1.13a
15: Boundary 1.13a/1.16b
16: Boundary 1.16b/1.17c
17: Boundary 1.17c/-
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
ENST00000236959
1a
ENSE00001914660
chr2:
216176540-216176884
345
PUR9_HUMAN
1-7
7
4
A:3-7
B:4-7
C:4-7
D:4-7
5
4
4
4
1.1g
ENST00000236959
1g
ENSE00001646681
chr2:
216177221-216177347
127
PUR9_HUMAN
7-49
43
4
A:7-49
B:7-49
C:7-49
D:7-49
43
43
43
43
1.2b
ENST00000236959
2b
ENSE00001806771
chr2:
216182880-216182956
77
PUR9_HUMAN
49-75
27
4
A:49-75
B:49-75
C:49-75
D:49-75
27
27
27
27
1.3
ENST00000236959
3
ENSE00001648662
chr2:
216184388-216184454
67
PUR9_HUMAN
75-97
23
4
A:75-97
B:75-97
C:75-97
D:75-97
23
23
23
23
1.4b
ENST00000236959
4b
ENSE00001712436
chr2:
216189964-216190052
89
PUR9_HUMAN
97-127
31
4
A:97-127
B:97-127
C:97-127
D:97-127
31
31
31
31
1.5b
ENST00000236959
5b
ENSE00001606333
chr2:
216190710-216190861
152
PUR9_HUMAN
127-177
51
4
A:127-177
B:127-177
C:127-177
D:127-177
51
51
51
51
1.6
ENST00000236959
6
ENSE00002173380
chr2:
216191545-216191701
157
PUR9_HUMAN
178-230
53
4
A:178-230
B:178-230
C:178-230
D:178-230
53
53
53
53
1.7
ENST00000236959
7
ENSE00001731167
chr2:
216197105-216197230
126
PUR9_HUMAN
230-272
43
4
A:230-272
B:230-272
C:230-272
D:230-272
43
43
43
43
1.8
ENST00000236959
8
ENSE00001775272
chr2:
216198073-216198180
108
PUR9_HUMAN
272-308
37
4
A:272-308
B:272-308
C:272-308
D:272-308
37
37
37
37
1.9b
ENST00000236959
9b
ENSE00001630599
chr2:
216199642-216199727
86
PUR9_HUMAN
308-336
29
4
A:308-336
B:308-336
C:308-336
D:308-336
29
29
29
29
1.10b
ENST00000236959
10b
ENSE00001620932
chr2:
216200758-216200847
90
PUR9_HUMAN
337-366
30
4
A:337-366
B:337-366
C:337-366
D:337-366
30
30
30
30
1.11c
ENST00000236959
11c
ENSE00001679432
chr2:
216203502-216203630
129
PUR9_HUMAN
367-409
43
4
A:367-409
B:367-409
C:367-409
D:367-409
43
43
43
43
1.12a
ENST00000236959
12a
ENSE00001642683
chr2:
216209502-216209594
93
PUR9_HUMAN
410-440
31
4
A:410-440
B:410-440
C:410-440
D:410-440
31
31
31
31
1.13a
ENST00000236959
13a
ENSE00001768906
chr2:
216211482-216211664
183
PUR9_HUMAN
441-501
61
4
A:441-501 (gaps)
B:441-501
C:441-501 (gaps)
D:441-501
61
61
61
61
1.16b
ENST00000236959
16b
ENSE00001703750
chr2:
216213817-216213972
156
PUR9_HUMAN
502-553
52
4
A:502-553
B:502-553
C:502-553
D:502-553
52
52
52
52
1.17c
ENST00000236959
17c
ENSE00001669993
chr2:
216214259-216214486
228
PUR9_HUMAN
554-592
39
4
A:554-592
B:554-592
C:554-592
D:554-592
39
39
39
39
[
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]
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1pkxa2 (A:201-592)
1b: SCOP_d1pkxb2 (B:201-592)
1c: SCOP_d1pkxc2 (C:201-592)
1d: SCOP_d1pkxd2 (D:201-592)
2a: SCOP_d1pkxa1 (A:3-200)
2b: SCOP_d1pkxb1 (B:4-200)
2c: SCOP_d1pkxc1 (C:4-200)
2d: SCOP_d1pkxd1 (D:4-200)
View:
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)
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Folds
(
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(
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(
)
(
)
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(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Cytidine deaminase-like
(78)
Superfamily
:
Cytidine deaminase-like
(76)
Family
:
AICAR transformylase domain of bifunctional purine biosynthesis enzyme ATIC
(12)
Protein domain
:
AICAR transformylase domain of bifunctional purine biosynthesis enzyme ATIC
(12)
Human (Homo sapiens) [TaxId: 9606]
(3)
1a
d1pkxa2
A:201-592
1b
d1pkxb2
B:201-592
1c
d1pkxc2
C:201-592
1d
d1pkxd2
D:201-592
Fold
:
Methylglyoxal synthase-like
(31)
Superfamily
:
Methylglyoxal synthase-like
(31)
Family
:
Inosicase
(12)
Protein domain
:
IMP cyclohydrolase domain of bifunctional purine biosynthesis enzyme ATIC
(12)
Human (Homo sapiens) [TaxId: 9606]
(3)
2a
d1pkxa1
A:3-200
2b
d1pkxb1
B:4-200
2c
d1pkxc1
C:4-200
2d
d1pkxd1
D:4-200
[
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]
CATH Domains
(3, 16)
Info
all CATH domains
1a: CATH_1pkxA02 (A:374-475,A:519-584)
1b: CATH_1pkxB02 (B:374-475,B:519-584)
1c: CATH_1pkxA03 (A:227-373)
1d: CATH_1pkxB03 (B:227-373)
1e: CATH_1pkxC03 (C:227-373)
1f: CATH_1pkxD03 (D:227-373)
1g: CATH_1pkxC02 (C:374-475,C:519-584)
1h: CATH_1pkxD02 (D:374-475,D:519-584)
2a: CATH_1pkxB04 (B:4-197)
2b: CATH_1pkxC04 (C:4-197)
2c: CATH_1pkxD04 (D:4-197)
2d: CATH_1pkxA04 (A:3-197)
3a: CATH_1pkxB01 (B:476-518)
3b: CATH_1pkxD01 (D:476-518)
3c: CATH_1pkxA01 (A:476-518)
3d: CATH_1pkxC01 (C:476-518)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Cytidine Deaminase; domain 2
(44)
Homologous Superfamily
:
[code=3.40.140.20, no name defined]
(11)
Human (Homo sapiens)
(3)
1a
1pkxA02
A:374-475,A:519-584
1b
1pkxB02
B:374-475,B:519-584
1c
1pkxA03
A:227-373
1d
1pkxB03
B:227-373
1e
1pkxC03
C:227-373
1f
1pkxD03
D:227-373
1g
1pkxC02
C:374-475,C:519-584
1h
1pkxD02
D:374-475,D:519-584
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.1380, no name defined]
(29)
Human (Homo sapiens)
(3)
2a
1pkxB04
B:4-197
2b
1pkxC04
C:4-197
2c
1pkxD04
D:4-197
2d
1pkxA04
A:3-197
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Helix Hairpins
(718)
Homologous Superfamily
:
[code=1.10.287.440, no name defined]
(11)
Human (Homo sapiens)
(3)
3a
1pkxB01
B:476-518
3b
1pkxD01
D:476-518
3c
1pkxA01
A:476-518
3d
1pkxC01
C:476-518
[
close CATH info
]
Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_AICARFT_IMPCHas_1pkxD01 (D:135-462)
1b: PFAM_AICARFT_IMPCHas_1pkxD02 (D:135-462)
1c: PFAM_AICARFT_IMPCHas_1pkxD03 (D:135-462)
1d: PFAM_AICARFT_IMPCHas_1pkxD04 (D:135-462)
2a: PFAM_MGS_1pkxD05 (D:16-130)
2b: PFAM_MGS_1pkxD06 (D:16-130)
2c: PFAM_MGS_1pkxD07 (D:16-130)
2d: PFAM_MGS_1pkxD08 (D:16-130)
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Clan
:
CDA
(39)
Family
:
AICARFT_IMPCHas
(5)
Homo sapiens (Human)
(1)
1a
AICARFT_IMPCHas-1pkxD01
D:135-462
1b
AICARFT_IMPCHas-1pkxD02
D:135-462
1c
AICARFT_IMPCHas-1pkxD03
D:135-462
1d
AICARFT_IMPCHas-1pkxD04
D:135-462
Clan
:
no clan defined [family: MGS]
(13)
Family
:
MGS
(13)
Homo sapiens (Human)
(2)
2a
MGS-1pkxD05
D:16-130
2b
MGS-1pkxD06
D:16-130
2c
MGS-1pkxD07
D:16-130
2d
MGS-1pkxD08
D:16-130
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