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1K9S
Asym. Unit
Info
Asym.Unit (252 KB)
Biol.Unit 1 (246 KB)
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(1)
Title
:
PURINE NUCLEOSIDE PHOSPHORYLASE FROM E. COLI IN COMPLEX WITH FORMYCIN A DERIVATIVE AND PHOSPHATE
Authors
:
G. Koellner, A. Bzowska, B. Wielgus-Kutrowska, M. Luic, T. Steiner, W. Saenger, J. Stepinski
Date
:
30 Oct 01 (Deposition) - 28 Nov 01 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Glycosyltransferase, Purine Nucleoside Phosphorylase, Transferase, E. Coli
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. Koellner, A. Bzowska, B. Wielgus-Kutrowska, M. Luic, T. Steiner, W. Saenger, J. Stepinski
Open And Closed Conformation Of The E. Coli Purine Nucleoside Phosphorylase Active Center And Implications For The Catalytic Mechanism.
J. Mol. Biol. V. 315 351 2002
(for further references see the
PDB file header
)
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Hetero Components
(3, 12)
Info
All Hetero Components
1a: 2-HYDROXYMETHYL-5-(7-METHYLAMINO-3... (FM1a)
1b: 2-HYDROXYMETHYL-5-(7-METHYLAMINO-3... (FM1b)
1c: 2-HYDROXYMETHYL-5-(7-METHYLAMINO-3... (FM1c)
2a: 2-(7-AMINO-6-METHYL-3H-PYRAZOLO[4,... (FM2a)
2b: 2-(7-AMINO-6-METHYL-3H-PYRAZOLO[4,... (FM2b)
2c: 2-(7-AMINO-6-METHYL-3H-PYRAZOLO[4,... (FM2c)
3a: PHOSPHATE ION (PO4a)
3b: PHOSPHATE ION (PO4b)
3c: PHOSPHATE ION (PO4c)
3d: PHOSPHATE ION (PO4d)
3e: PHOSPHATE ION (PO4e)
3f: PHOSPHATE ION (PO4f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FM1
3
Ligand/Ion
2-HYDROXYMETHYL-5-(7-METHYLAMINO-3H-PYRAZOLO[4,3-D]PYRIMIDIN-3-YL)-TETRAHYDRO-FURAN-3,4-DIOL
2
FM2
3
Ligand/Ion
2-(7-AMINO-6-METHYL-3H-PYRAZOLO[4,3-D]PYRIMIDIN-3-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL
3
PO4
6
Ligand/Ion
PHOSPHATE ION
[
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Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:20 , ARG A:24 , ARG A:87 , GLY A:89 , SER A:90 , FM2 A:9901 , ARG D:43
BINDING SITE FOR RESIDUE PO4 A 9902
02
AC2
SOFTWARE
MET A:64 , ARG A:87 , SER A:90 , CYS A:91 , GLY A:92 , PHE A:159 , VAL A:178 , GLU A:179 , MET A:180 , GLU A:181 , SER A:203 , ASP A:204 , HOH A:1022 , HOH A:1082 , PO4 A:9902 , HIS D:4 , ARG D:43
BINDING SITE FOR RESIDUE FM2 A 9901
03
AC3
SOFTWARE
GLY B:20 , ARG B:24 , ARG B:87 , GLY B:89 , SER B:90 , FM2 B:9903 , ARG E:43
BINDING SITE FOR RESIDUE PO4 B 9904
04
AC4
SOFTWARE
MET B:64 , ARG B:87 , SER B:90 , CYS B:91 , GLY B:92 , PHE B:159 , VAL B:178 , GLU B:179 , MET B:180 , GLU B:181 , SER B:203 , ASP B:204 , HOH B:1022 , HOH B:1109 , PO4 B:9904 , HIS E:4 , ARG E:43
BINDING SITE FOR RESIDUE FM2 B 9903
05
AC5
SOFTWARE
GLY C:20 , ARG C:24 , ARG C:87 , GLY C:89 , SER C:90 , FM2 C:9905 , ARG F:43
BINDING SITE FOR RESIDUE PO4 C 9906
06
AC6
SOFTWARE
MET C:64 , ARG C:87 , SER C:90 , CYS C:91 , GLY C:92 , PHE C:159 , VAL C:178 , GLU C:179 , MET C:180 , GLU C:181 , SER C:203 , ASP C:204 , HOH C:1026 , HOH C:1079 , PO4 C:9906 , HIS F:4 , ARG F:43
BINDING SITE FOR RESIDUE FM2 C 9905
07
AC7
SOFTWARE
ARG A:43 , PRO D:19 , GLY D:20 , ARG D:24 , ARG D:87 , GLY D:89 , SER D:90 , FM1 D:9907
BINDING SITE FOR RESIDUE PO4 D 9908
08
AC8
SOFTWARE
HIS A:4 , ARG A:43 , ARG D:87 , SER D:90 , CYS D:91 , GLY D:92 , PHE D:159 , VAL D:178 , GLU D:179 , MET D:180 , GLU D:181 , ASP D:204 , ILE D:206 , HOH D:1070 , HOH D:1098 , PO4 D:9908 , HOH D:9927
BINDING SITE FOR RESIDUE FM1 D 9907
09
AC9
SOFTWARE
ARG B:43 , GLY E:20 , ARG E:24 , ARG E:87 , GLY E:89 , SER E:90 , FM1 E:9909
BINDING SITE FOR RESIDUE PO4 E 9910
10
BC1
SOFTWARE
HIS B:4 , ARG B:43 , MET E:64 , ARG E:87 , SER E:90 , CYS E:91 , GLY E:92 , PHE E:159 , VAL E:178 , GLU E:179 , MET E:180 , GLU E:181 , ASP E:204 , ILE E:206 , HOH E:1059 , PO4 E:9910 , HOH E:9919
BINDING SITE FOR RESIDUE FM1 E 9909
11
BC2
SOFTWARE
ARG C:43 , PRO F:19 , GLY F:20 , ARG F:24 , ARG F:87 , GLY F:89 , SER F:90 , FM1 F:9911
BINDING SITE FOR RESIDUE PO4 F 9912
12
BC3
SOFTWARE
HIS C:4 , ARG C:43 , MET F:64 , ARG F:87 , SER F:90 , CYS F:91 , GLY F:92 , PHE F:159 , VAL F:178 , GLU F:179 , MET F:180 , GLU F:181 , SER F:203 , ASP F:204 , HOH F:1036 , HOH F:1063 , HOH F:1064 , PO4 F:9912
BINDING SITE FOR RESIDUE FM1 F 9911
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 6)
Info
All PROSITE Patterns/Profiles
1: PNP_UDP_1 (A:61-76,B:61-76,C:61-76,D:61-76,E:...)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PNP_UDP_1
PS01232
Purine and other phosphorylases family 1 signature.
DEOD_ECOLI
62-77
6
A:61-76
B:61-76
C:61-76
D:61-76
E:61-76
F:61-76
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Exons
(0, 0)
Info
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d1k9sa_ (A:)
1b: SCOP_d1k9sb_ (B:)
1c: SCOP_d1k9sc_ (C:)
1d: SCOP_d1k9sd_ (D:)
1e: SCOP_d1k9se_ (E:)
1f: SCOP_d1k9sf_ (F:)
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Protein Domains
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)
(
)
Organisms
(
)
(
)
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)
Escherichia coli [TaxId: 562]
(24)
1a
d1k9sa_
A:
1b
d1k9sb_
B:
1c
d1k9sc_
C:
1d
d1k9sd_
D:
1e
d1k9se_
E:
1f
d1k9sf_
F:
[
close SCOP info
]
CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_1k9sA00 (A:1-237)
1b: CATH_1k9sB00 (B:1-237)
1c: CATH_1k9sC00 (C:1-237)
1d: CATH_1k9sD00 (D:1-237)
1e: CATH_1k9sE00 (E:1-237)
1f: CATH_1k9sF00 (F:1-237)
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Homologous Superfamilies
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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)
Escherichia coli. Organism_taxid: 562
(2)
1a
1k9sA00
A:1-237
1b
1k9sB00
B:1-237
1c
1k9sC00
C:1-237
1d
1k9sD00
D:1-237
1e
1k9sE00
E:1-237
1f
1k9sF00
F:1-237
[
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Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_PNP_UDP_1_1k9sF01 (F:14-233)
1b: PFAM_PNP_UDP_1_1k9sF02 (F:14-233)
1c: PFAM_PNP_UDP_1_1k9sF03 (F:14-233)
1d: PFAM_PNP_UDP_1_1k9sF04 (F:14-233)
1e: PFAM_PNP_UDP_1_1k9sF05 (F:14-233)
1f: PFAM_PNP_UDP_1_1k9sF06 (F:14-233)
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Clan
:
PUP
(121)
Family
:
PNP_UDP_1
(121)
Escherichia coli (strain K12)
(27)
1a
PNP_UDP_1-1k9sF01
F:14-233
1b
PNP_UDP_1-1k9sF02
F:14-233
1c
PNP_UDP_1-1k9sF03
F:14-233
1d
PNP_UDP_1-1k9sF04
F:14-233
1e
PNP_UDP_1-1k9sF05
F:14-233
1f
PNP_UDP_1-1k9sF06
F:14-233
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