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2WK5
Asym. Unit
Info
Asym.Unit (267 KB)
Biol.Unit 1 (68 KB)
Biol.Unit 2 (68 KB)
Biol.Unit 3 (69 KB)
Biol.Unit 4 (69 KB)
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(1)
Title
:
STRUCTURAL FEATURES OF NATIVE HUMAN THYMIDINE PHOSPHORYLASE AND IN COMPLEX WITH 5-IODOURACIL
Authors
:
E. Mitsiki, A. C. Papageorgiou, S. Iyer, N. Thiyagarajan, S. H. Prior, D. Sleep, C. Finnis, K. R. Acharya
Date
:
05 Jun 09 (Deposition) - 07 Jul 09 (Release) - 28 Jul 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.99
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Glycosyltransferase, Developmental Protein, Angiogenesis, 5-Iodouracil, Growth Factor, Enzyme Kinetics, Differentiation, Disease Mutation, Thymidine Phosphorylase, Chemotaxis, Transferase, Mutagenesis, Polymorphism
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Mitsiki, A. C. Papageorgiou, S. Iyer, N. Thiyagarajan, S. H. Prior, D. Sleep, C. Finnis, K. R. Acharya
Structures Of Native Human Thymidine Phosphorylase And In Complex With 5-Iodouracil.
Biochem. Biophys. Res. Commun. V. 386 666 2009
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
1
Ligand/Ion
GLYCEROL
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Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP B:304 , HOH B:2006 , HOH B:2007
BINDING SITE FOR RESIDUE GOL B1481
[
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]
SAPs(SNPs)/Variants
(6, 24)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_016777 (R44Q, chain A/B/C/D, )
2: VAR_007643 (G145R, chain A/B/C/D, )
3: VAR_007644 (G153S, chain A/B/C/D, )
4: VAR_007645 (K222R, chain A/B/C/D, )
5: VAR_007646 (E289A, chain A/B/C/D, )
6: VAR_007648 (S471L, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_016777
R
44
Q
TYPH_HUMAN
Disease (MTDPS1)
---
A/B/C/D
R
44
Q
2
UniProt
VAR_007643
G
145
R
TYPH_HUMAN
Disease (MTDPS1)
---
A/B/C/D
G
145
R
3
UniProt
VAR_007644
G
153
S
TYPH_HUMAN
Disease (MTDPS1)
---
A/B/C/D
G
153
S
4
UniProt
VAR_007645
K
222
R
TYPH_HUMAN
Disease (MTDPS1)
---
A/B/C/D
K
222
R
5
UniProt
VAR_007646
E
289
A
TYPH_HUMAN
Disease (MTDPS1)
---
A/B/C/D
E
289
A
6
UniProt
VAR_007648
S
471
L
TYPH_HUMAN
Polymorphism
11479
A/B/C/D
S
471
L
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: THYMID_PHOSPHORYLASE (A:144-159,B:144-159,C:144-159,D:14...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
THYMID_PHOSPHORYLASE
PS00647
Thymidine and pyrimidine-nucleoside phosphorylases signature.
TYPH_HUMAN
144-159
4
A:144-159
B:144-159
C:144-159
D:144-159
[
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]
Exons
(9, 36)
Info
All Exons
Exon 1.1j (A:32-72 | B:32-72 | C:33-72 | D:34...)
Exon 1.1o (A:72-139 | B:72-139 (gaps) | C:72-...)
Exon 1.1p (A:140-172 | B:140-172 | C:140-172 ...)
Exon 1.2a (A:173-216 | B:173-216 | C:173-216 ...)
Exon 1.3 (A:216-255 | B:216-255 | C:216-255 ...)
Exon 1.4 (A:256-310 | B:256-310 | C:256-310 ...)
Exon 1.5a (A:310-387 | B:310-387 | C:310-387 ...)
Exon 1.5d (A:387-434 | B:387-434 | C:387-434 ...)
Exon 1.6e (A:434-480 | B:434-481 | C:434-480 ...)
View:
Select:
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All Exon Boundaries
01: Boundary 1.1g/1.1j
02: Boundary 1.1j/1.1o
03: Boundary 1.1o/1.1p
04: Boundary 1.1p/1.2a
05: Boundary 1.2a/1.3
06: Boundary 1.3/1.4
07: Boundary 1.4/1.5a
08: Boundary 1.5a/1.5d
09: Boundary 1.5d/1.6e
10: Boundary 1.6e/-
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
1.1g
ENST00000395680
1g
ENSE00001522468
chr22:
50968428-50968333
96
TYPH_HUMAN
-
0
0
-
-
1.1j
ENST00000395680
1j
ENSE00001522466
chr22:
50968183-50967925
259
TYPH_HUMAN
1-72
72
4
A:32-72
B:32-72
C:33-72
D:34-72
41
41
40
39
1.1o
ENST00000395680
1o
ENSE00000657761
chr22:
50967767-50967565
203
TYPH_HUMAN
72-139
68
4
A:72-139
B:72-139 (gaps)
C:72-139
D:72-139 (gaps)
68
68
68
68
1.1p
ENST00000395680
1p
ENSE00000657760
chr22:
50967039-50966941
99
TYPH_HUMAN
140-172
33
4
A:140-172
B:140-172
C:140-172
D:140-172
33
33
33
33
1.2a
ENST00000395680
2a
ENSE00000657759
chr22:
50966146-50966017
130
TYPH_HUMAN
173-216
44
4
A:173-216
B:173-216
C:173-216
D:173-216
44
44
44
44
1.3
ENST00000395680
3
ENSE00000878932
chr22:
50965712-50965594
119
TYPH_HUMAN
216-255
40
4
A:216-255
B:216-255
C:216-255
D:216-255
40
40
40
40
1.4
ENST00000395680
4
ENSE00000657757
chr22:
50965167-50965005
163
TYPH_HUMAN
256-310
55
4
A:256-310
B:256-310
C:256-310
D:256-310
55
55
55
55
1.5a
ENST00000395680
5a
ENSE00000657756
chr22:
50964905-50964675
231
TYPH_HUMAN
310-387
78
4
A:310-387
B:310-387
C:310-387
D:310-387 (gaps)
78
78
78
78
1.5d
ENST00000395680
5d
ENSE00000657754
chr22:
50964570-50964430
141
TYPH_HUMAN
387-434
48
4
A:387-434
B:387-434
C:387-434
D:387-434
48
48
48
48
1.6e
ENST00000395680
6e
ENSE00000878931
chr22:
50964347-50964181
167
TYPH_HUMAN
434-482
49
4
A:434-480
B:434-481
C:434-480 (gaps)
D:434-480
47
48
47
47
[
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]
SCOP Domains
(3, 12)
Info
All SCOP Domains
1a: SCOP_d2wk5a1 (A:32-100)
1b: SCOP_d2wk5b1 (B:32-100)
1c: SCOP_d2wk5c1 (C:33-100)
1d: SCOP_d2wk5d1 (D:34-100)
2a: SCOP_d2wk5a3 (A:374-480)
2b: SCOP_d2wk5b3 (B:374-481)
2c: SCOP_d2wk5c3 (C:374-480)
2d: SCOP_d2wk5d3 (D:374-480)
3a: SCOP_d2wk5a2 (A:101-373)
3b: SCOP_d2wk5b2 (B:101-373)
3c: SCOP_d2wk5c2 (C:101-373)
3d: SCOP_d2wk5d2 (D:101-373)
View:
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Classes
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)
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Folds
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(
)
Superfamilies
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)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Methionine synthase domain-like
(29)
Superfamily
:
Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain
(22)
Family
:
automated matches
(3)
Protein domain
:
automated matches
(3)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d2wk5a1
A:32-100
1b
d2wk5b1
B:32-100
1c
d2wk5c1
C:33-100
1d
d2wk5d1
D:34-100
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
alpha/beta-Hammerhead
(191)
Superfamily
:
Pyrimidine nucleoside phosphorylase C-terminal domain
(12)
Family
:
automated matches
(3)
Protein domain
:
automated matches
(3)
Human (Homo sapiens) [TaxId: 9606]
(2)
2a
d2wk5a3
A:374-480
2b
d2wk5b3
B:374-481
2c
d2wk5c3
C:374-480
2d
d2wk5d3
D:374-480
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain
(22)
Superfamily
:
Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain
(22)
Family
:
Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain
(21)
Protein domain
:
automated matches
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
3a
d2wk5a2
A:101-373
3b
d2wk5b2
B:101-373
3c
d2wk5c2
C:101-373
3d
d2wk5d2
D:101-373
[
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]
CATH Domains
(3, 12)
Info
all CATH domains
1a: CATH_2wk5D02 (D:101-371,D:468-480)
1b: CATH_2wk5A02 (A:101-371,A:468-480)
1c: CATH_2wk5B02 (B:101-371,B:468-481)
1d: CATH_2wk5C02 (C:101-371,C:469-480)
2a: CATH_2wk5A03 (A:372-467)
2b: CATH_2wk5C03 (C:372-465)
2c: CATH_2wk5B03 (B:372-467)
2d: CATH_2wk5D03 (D:372-467)
3a: CATH_2wk5A01 (A:32-100)
3b: CATH_2wk5D01 (D:34-100)
3c: CATH_2wk5B01 (B:32-100)
3d: CATH_2wk5C01 (C:33-100)
View:
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Topologies
(
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(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2
(23)
Homologous Superfamily
:
Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2
(23)
Human (Homo sapiens)
(4)
1a
2wk5D02
D:101-371,D:468-480
1b
2wk5A02
A:101-371,A:468-480
1c
2wk5B02
B:101-371,B:468-481
1d
2wk5C02
C:101-371,C:469-480
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Aldehyde Oxidoreductase; domain 3
(111)
Homologous Superfamily
:
[code=3.90.1170.30, no name defined]
(10)
Human (Homo sapiens)
(4)
2a
2wk5A03
A:372-467
2b
2wk5C03
C:372-465
2c
2wk5B03
B:372-467
2d
2wk5D03
D:372-467
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3
(19)
Homologous Superfamily
:
Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C
(18)
Human (Homo sapiens)
(4)
3a
2wk5A01
A:32-100
3b
2wk5D01
D:34-100
3c
2wk5B01
B:32-100
3d
2wk5C01
C:33-100
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Chain D
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Asym.Unit (267 KB)
Header - Asym.Unit
Biol.Unit 1 (68 KB)
Header - Biol.Unit 1
Biol.Unit 2 (68 KB)
Header - Biol.Unit 2
Biol.Unit 3 (69 KB)
Header - Biol.Unit 3
Biol.Unit 4 (69 KB)
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