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1LVU
Asym. Unit
Info
Asym.Unit (309 KB)
Biol.Unit 1 (301 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF CALF SPLEEN PURINE NUCLEOSIDE PHOSPHORYLASE IN A NEW SPACE GROUP WITH FULL TRIMER IN THE ASYMMETRIC UNIT
Authors
:
A. Bzowska, G. Koellner, B. Wielgus-Kutrowska, A. Stroh, G. Raszewski, A. Holy, T. Steiner, J. Frank
Date
:
29 May 02 (Deposition) - 02 Sep 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.05
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Pnp, Purie Nucleoside Phosphorylase, Pentosyltransferase, New Space Group, 2, 6-Diaminopurine Multisubstrate Analogue Inhibitor
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Bzowska, G. Koellner, B. Wielgus-Kutrowska, A. Stroh, G. Raszewski, A. Holy, T. Steiner, J. Frank
Crystal Structure Of Calf Spleen Purine Nucleoside Phosphorylase With Two Full Trimers In The Asymmetric Unit: Important Implications For The Mechanism Of Catalysis
J. Mol. Biol. V. 342 1015 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 16)
Info
All Hetero Components
1a: 2,6-DIAMINO-(S)-9-[2-(PHOSPHONOMET... (9PPa)
1b: 2,6-DIAMINO-(S)-9-[2-(PHOSPHONOMET... (9PPb)
1c: 2,6-DIAMINO-(S)-9-[2-(PHOSPHONOMET... (9PPc)
1d: 2,6-DIAMINO-(S)-9-[2-(PHOSPHONOMET... (9PPd)
1e: 2,6-DIAMINO-(S)-9-[2-(PHOSPHONOMET... (9PPe)
1f: 2,6-DIAMINO-(S)-9-[2-(PHOSPHONOMET... (9PPf)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
2e: CALCIUM ION (CAe)
2f: CALCIUM ION (CAf)
2g: CALCIUM ION (CAg)
2h: CALCIUM ION (CAh)
2i: CALCIUM ION (CAi)
2j: CALCIUM ION (CAj)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
9PP
6
Ligand/Ion
2,6-DIAMINO-(S)-9-[2-(PHOSPHONOMETHOXY)PROPYL]PURINE
2
CA
10
Ligand/Ion
CALCIUM ION
[
close Hetero Component info
]
Sites
(16, 16)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:51 , GLU A:58 , HOH A:8018 , HOH A:8022 , HOH A:8094 , GLU D:58
BINDING SITE FOR RESIDUE CA A 8001
02
AC2
SOFTWARE
GLU A:58 , SER D:51 , GLU D:58 , HOH D:8044 , HOH D:8058 , HOH D:8154
BINDING SITE FOR RESIDUE CA D 8002
03
AC3
SOFTWARE
GLU B:1058 , HOH B:8073 , HOH F:204 , HOH F:306 , SER F:2051 , GLU F:2058
BINDING SITE FOR RESIDUE CA F 8003
04
AC4
SOFTWARE
SER B:1051 , GLU B:1058 , HOH B:8022 , HOH B:8052 , HOH B:8071 , GLU F:2058
BINDING SITE FOR RESIDUE CA B 8004
05
AC5
SOFTWARE
HOH C:117 , HOH C:355 , SER C:2051 , GLU C:2058 , GLU E:1058 , HOH E:8072
BINDING SITE FOR RESIDUE CA C 8005
06
AC6
SOFTWARE
GLU C:2058 , SER E:1051 , GLU E:1058 , HOH E:8042 , HOH E:8059 , HOH E:8090
BINDING SITE FOR RESIDUE CA E 8006
07
AC7
SOFTWARE
ASP B:1215 , HOH B:8043 , HOH B:8244 , HOH B:8337 , GLU D:250
BINDING SITE FOR RESIDUE CA B 8007
08
AC8
SOFTWARE
GLU C:2250 , HOH F:76 , HOH F:582 , ASN F:2121 , ASP F:2215
BINDING SITE FOR RESIDUE CA F 8008
09
AC9
SOFTWARE
GLU A:8 , HOH A:8082 , HOH A:8091 , GLU E:1008 , HOH E:8032 , HOH E:8274
BINDING SITE FOR RESIDUE CA A 8009
10
BC1
SOFTWARE
GLU B:1008 , HOH B:8037 , HOH B:8131 , GLU D:8 , HOH D:8033 , HOH D:8131
BINDING SITE FOR RESIDUE CA B 8010
11
BC2
SOFTWARE
GLY A:32 , SER A:33 , HIS A:86 , ASN A:115 , ALA A:116 , GLY A:118 , LEU A:195 , PHE A:200 , GLU A:201 , VAL A:217 , GLY A:218 , MET A:219 , SER A:220 , ASN A:243 , HOH A:8034 , HOH A:8048 , HOH A:8070 , HOH A:8092 , HOH A:8131 , HOH A:8162
BINDING SITE FOR RESIDUE 9PP A 6100
12
BC3
SOFTWARE
GLY B:1032 , SER B:1033 , ARG B:1084 , HIS B:1086 , ASN B:1115 , ALA B:1116 , ALA B:1117 , GLY B:1118 , LEU B:1195 , PHE B:1200 , GLU B:1201 , VAL B:1217 , GLY B:1218 , MET B:1219 , SER B:1220 , ASN B:1243 , HOH B:8012 , HOH B:8057 , HOH B:8092 , HOH B:8105 , HOH B:8119
BINDING SITE FOR RESIDUE 9PP B 6200
13
BC4
SOFTWARE
HOH C:134 , HOH C:326 , HOH C:483 , HOH C:707 , HOH C:1653 , GLY C:2032 , SER C:2033 , ARG C:2084 , HIS C:2086 , ASN C:2115 , ALA C:2116 , ALA C:2117 , GLY C:2118 , PHE C:2200 , GLU C:2201 , VAL C:2217 , GLY C:2218 , MET C:2219 , SER C:2220 , ASN C:2243
BINDING SITE FOR RESIDUE 9PP C 6300
14
BC5
SOFTWARE
GLY D:32 , SER D:33 , HIS D:86 , ASN D:115 , ALA D:116 , ALA D:117 , GLY D:118 , LEU D:195 , PHE D:200 , GLU D:201 , VAL D:217 , GLY D:218 , MET D:219 , SER D:220 , ASN D:243 , HOH D:8019 , HOH D:8024 , HOH D:8056 , HOH D:8083 , HOH D:8123
BINDING SITE FOR RESIDUE 9PP D 6400
15
BC6
SOFTWARE
GLY E:1032 , SER E:1033 , ARG E:1084 , HIS E:1086 , ASN E:1115 , ALA E:1116 , ALA E:1117 , GLY E:1118 , LEU E:1195 , PHE E:1200 , GLU E:1201 , VAL E:1217 , GLY E:1218 , MET E:1219 , SER E:1220 , ASN E:1243 , HOH E:8016 , HOH E:8022 , HOH E:8030 , HOH E:8051 , HOH E:8056 , PHE F:2159
BINDING SITE FOR RESIDUE 9PP E 6500
16
BC7
SOFTWARE
HOH F:157 , HOH F:276 , HOH F:279 , HOH F:860 , GLY F:2032 , SER F:2033 , HIS F:2086 , ASN F:2115 , ALA F:2116 , ALA F:2117 , GLY F:2118 , LEU F:2195 , PHE F:2200 , GLU F:2201 , VAL F:2217 , GLY F:2218 , MET F:2219 , SER F:2220 , ASN F:2243
BINDING SITE FOR RESIDUE 9PP F 6600
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 6)
Info
All PROSITE Patterns/Profiles
1: PNP_MTAP_2 (A:79-120,B:1079-1120,C:2079-2120,D...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PNP_MTAP_2
PS01240
Purine and other phosphorylases family 2 signature.
PNPH_BOVIN
79-120
6
A:79-120
B:1079-1120
C:2079-2120
D:79-120
E:1079-1120
F:2079-2120
[
close PROSITE info
]
Exons
(6, 36)
Info
All Exons
Exon 1.1 (A:2-33 | B:1002-1033 | C:2001-2033...)
Exon 1.3 (A:33-90 | B:1033-1090 | C:2033-209...)
Exon 1.4 (A:90-124 | B:1090-1124 | C:2090-21...)
Exon 1.5 (A:125-183 | B:1125-1183 | C:2125-2...)
Exon 1.6 (A:183-247 | B:1183-1247 | C:2183-2...)
Exon 1.7 (A:247-284 (gaps) | B:1247-1284 (ga...)
View:
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All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/1.3
3: Boundary 1.3/1.4
4: Boundary 1.4/1.5
5: Boundary 1.5/1.6
6: Boundary 1.6/1.7
7: Boundary 1.7/-
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
1.1
ENSBTAT00000016346
1
ENSBTAE00000133169
chr10:
26040769-26040670
100
PNPH_BOVIN
1-33
33
6
A:2-33
B:1002-1033
C:2001-2033
D:2-33
E:1002-1033
F:2001-2033
32
32
33
32
32
33
1.3
ENSBTAT00000016346
3
ENSBTAE00000420054
chr10:
26038796-26038627
170
PNPH_BOVIN
33-90
58
6
A:33-90
B:1033-1090
C:2033-2090
D:33-90
E:1033-1090
F:2033-2090
58
58
58
58
58
58
1.4
ENSBTAT00000016346
4
ENSBTAE00000408817
chr10:
26036665-26036562
104
PNPH_BOVIN
90-124
35
6
A:90-124
B:1090-1124
C:2090-2124
D:90-124
E:1090-1124
F:2090-2124
35
35
35
35
35
35
1.5
ENSBTAT00000016346
5
ENSBTAE00000427656
chr10:
26036357-26036182
176
PNPH_BOVIN
125-183
59
6
A:125-183
B:1125-1183
C:2125-2183
D:125-183
E:1125-1183
F:2125-2183
59
59
59
59
59
59
1.6
ENSBTAT00000016346
6
ENSBTAE00000404946
chr10:
26036090-26035900
191
PNPH_BOVIN
183-247
65
6
A:183-247
B:1183-1247
C:2183-2247
D:183-247
E:1183-1247
F:2183-2247
65
65
65
65
65
65
1.7
ENSBTAT00000016346
7
ENSBTAE00000133178
chr10:
26035106-26034471
636
PNPH_BOVIN
247-318
72
6
A:247-284 (gaps)
B:1247-1284 (gaps)
C:2247-2284 (gaps)
D:247-284 (gaps)
E:1247-1284 (gaps)
F:2247-2284 (gaps)
38
38
38
38
38
38
[
close EXON info
]
SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d1lvua_ (A:)
1b: SCOP_d1lvub_ (B:)
1c: SCOP_d1lvuc_ (C:)
1d: SCOP_d1lvud_ (D:)
1e: SCOP_d1lvue_ (E:)
1f: SCOP_d1lvuf_ (F:)
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Organisms
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)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Phosphorylase/hydrolase-like
(558)
Superfamily
:
Purine and uridine phosphorylases
(283)
Family
:
Purine and uridine phosphorylases
(224)
Protein domain
:
Purine nucleoside phosphorylase, PNP
(93)
Cow (Bos taurus) [TaxId: 9913]
(20)
1a
d1lvua_
A:
1b
d1lvub_
B:
1c
d1lvuc_
C:
1d
d1lvud_
D:
1e
d1lvue_
E:
1f
d1lvuf_
F:
[
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CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_1lvuE00 (E:1002-1284)
1b: CATH_1lvuF00 (F:2001-2284)
1c: CATH_1lvuA00 (A:2-284)
1d: CATH_1lvuC00 (C:2001-2284)
1e: CATH_1lvuB00 (B:1002-1284)
1f: CATH_1lvuD00 (D:2-284)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.1580, no name defined]
(194)
Cattle (Bos taurus)
(20)
1a
1lvuE00
E:1002-1284
1b
1lvuF00
F:2001-2284
1c
1lvuA00
A:2-284
1d
1lvuC00
C:2001-2284
1e
1lvuB00
B:1002-1284
1f
1lvuD00
D:2-284
[
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Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_PNP_UDP_1_1lvuF01 (F:2026-2280)
1b: PFAM_PNP_UDP_1_1lvuF02 (F:2026-2280)
1c: PFAM_PNP_UDP_1_1lvuF03 (F:2026-2280)
1d: PFAM_PNP_UDP_1_1lvuF04 (F:2026-2280)
1e: PFAM_PNP_UDP_1_1lvuF05 (F:2026-2280)
1f: PFAM_PNP_UDP_1_1lvuF06 (F:2026-2280)
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Clan
:
PUP
(121)
Family
:
PNP_UDP_1
(121)
Bos taurus (Bovine)
(11)
1a
PNP_UDP_1-1lvuF01
F:2026-2280
1b
PNP_UDP_1-1lvuF02
F:2026-2280
1c
PNP_UDP_1-1lvuF03
F:2026-2280
1d
PNP_UDP_1-1lvuF04
F:2026-2280
1e
PNP_UDP_1-1lvuF05
F:2026-2280
1f
PNP_UDP_1-1lvuF06
F:2026-2280
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