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1T8S
Asym. Unit
Info
Asym.Unit (442 KB)
Biol.Unit 1 (433 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF E.COLI AMP NUCLEOSIDASE COMPLEXED WITH FORMICIN 5'-MONOPHOSPHATE
Authors
:
Y. Zhang, S. E. Cottet, S. E. Ealick
Date
:
13 May 04 (Deposition) - 17 Aug 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Alpha-Beta-Alpha Sandwich, Alpha-Beta Fold, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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)
Reference
:
Y. Zhang, S. E. Cottet, S. E. Ealick
Structure Of Escherichia Coli Amp Nucleosidase Reveals Similarity To Nucleoside Phosphorylases
Structure V. 12 1383 2004
(for further references see the
PDB file header
)
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Hetero Components
(2, 30)
Info
All Hetero Components
1a: FORMYCIN-5'-MONOPHOSPHATE (FMPa)
1b: FORMYCIN-5'-MONOPHOSPHATE (FMPb)
1c: FORMYCIN-5'-MONOPHOSPHATE (FMPc)
1d: FORMYCIN-5'-MONOPHOSPHATE (FMPd)
1e: FORMYCIN-5'-MONOPHOSPHATE (FMPe)
1f: FORMYCIN-5'-MONOPHOSPHATE (FMPf)
2a: SELENOMETHIONINE (MSEa)
2b: SELENOMETHIONINE (MSEb)
2c: SELENOMETHIONINE (MSEc)
2d: SELENOMETHIONINE (MSEd)
2e: SELENOMETHIONINE (MSEe)
2f: SELENOMETHIONINE (MSEf)
2g: SELENOMETHIONINE (MSEg)
2h: SELENOMETHIONINE (MSEh)
2i: SELENOMETHIONINE (MSEi)
2j: SELENOMETHIONINE (MSEj)
2k: SELENOMETHIONINE (MSEk)
2l: SELENOMETHIONINE (MSEl)
2m: SELENOMETHIONINE (MSEm)
2n: SELENOMETHIONINE (MSEn)
2o: SELENOMETHIONINE (MSEo)
2p: SELENOMETHIONINE (MSEp)
2q: SELENOMETHIONINE (MSEq)
2r: SELENOMETHIONINE (MSEr)
2s: SELENOMETHIONINE (MSEs)
2t: SELENOMETHIONINE (MSEt)
2u: SELENOMETHIONINE (MSEu)
2v: SELENOMETHIONINE (MSEv)
2w: SELENOMETHIONINE (MSEw)
2x: SELENOMETHIONINE (MSEx)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FMP
6
Ligand/Ion
FORMYCIN-5'-MONOPHOSPHATE
2
MSE
24
Mod. Amino Acid
SELENOMETHIONINE
[
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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
ASN A:205 , CYS A:306 , GLY A:307 , ARG A:381 , TRP A:383 , ASP A:403 , MSE A:404 , GLU A:405 , ASP A:428 , PRO A:430 , LYS A:436 , HIS B:188 , TYR B:189
BINDING SITE FOR RESIDUE FMP A 501
2
AC2
SOFTWARE
HIS A:188 , TYR A:189 , HOH A:522 , ASN B:205 , HIS B:305 , CYS B:306 , GLY B:307 , ARG B:381 , TRP B:383 , ASP B:403 , MSE B:404 , GLU B:405 , ASP B:428 , PRO B:430 , LYS B:436
BINDING SITE FOR RESIDUE FMP B 502
3
AC3
SOFTWARE
ASN C:205 , CYS C:306 , GLY C:307 , ARG C:381 , TRP C:383 , ILE C:402 , ASP C:403 , MSE C:404 , GLU C:405 , ASP C:428 , PRO C:430 , LYS C:436 , HIS D:188 , TYR D:189 , HOH D:507
BINDING SITE FOR RESIDUE FMP C 503
4
AC4
SOFTWARE
HIS C:188 , TYR C:189 , HOH C:510 , ASN D:205 , CYS D:306 , GLY D:307 , ARG D:381 , TRP D:383 , ASP D:403 , MSE D:404 , GLU D:405 , ASP D:428 , PRO D:430 , LYS D:436
BINDING SITE FOR RESIDUE FMP D 504
5
AC5
SOFTWARE
ASN E:205 , CYS E:306 , GLY E:307 , ARG E:381 , TRP E:383 , ASP E:403 , MSE E:404 , GLU E:405 , ASP E:428 , PRO E:430 , LYS E:436 , HOH E:509 , HIS F:188 , TYR F:189
BINDING SITE FOR RESIDUE FMP E 505
6
AC6
SOFTWARE
HIS E:188 , TYR E:189 , ASN F:205 , CYS F:306 , GLY F:307 , ARG F:381 , TRP F:383 , ASP F:403 , MSE F:404 , GLU F:405 , ASP F:428 , PRO F:430 , LYS F:436
BINDING SITE FOR RESIDUE FMP F 506
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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End label:
Sorry, no Info available
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Exons
(0, 0)
Info
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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.
SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d1t8sa_ (A:)
1b: SCOP_d1t8sb_ (B:)
1c: SCOP_d1t8sc_ (C:)
1d: SCOP_d1t8sd_ (D:)
1e: SCOP_d1t8se_ (E:)
1f: SCOP_d1t8sf_ (F:)
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)
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)
(
)
Protein Domains
(
)
(
)
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
:
AMP nucleosidase
(5)
Escherichia coli [TaxId: 562]
(4)
1a
d1t8sa_
A:
1b
d1t8sb_
B:
1c
d1t8sc_
C:
1d
d1t8sd_
D:
1e
d1t8se_
E:
1f
d1t8sf_
F:
[
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CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_1t8sA01 (A:8-172)
1b: CATH_1t8sB01 (B:8-172)
1c: CATH_1t8sC01 (C:8-172)
1d: CATH_1t8sD01 (D:8-172)
1e: CATH_1t8sE01 (E:8-172)
1f: CATH_1t8sF01 (F:8-172)
2a: CATH_1t8sA02 (A:173-484)
2b: CATH_1t8sC02 (C:173-484)
2c: CATH_1t8sD02 (D:173-484)
2d: CATH_1t8sE02 (E:173-484)
2e: CATH_1t8sF02 (F:173-484)
2f: CATH_1t8sB02 (B:173-484)
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(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
amp nucleosidase, domain 1
(5)
Homologous Superfamily
:
amp nucleosidase, domain 1
(5)
Escherichia coli. Organism_taxid: 562.
(4)
1a
1t8sA01
A:8-172
1b
1t8sB01
B:8-172
1c
1t8sC01
C:8-172
1d
1t8sD01
D:8-172
1e
1t8sE01
E:8-172
1f
1t8sF01
F:8-172
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.
(30)
2a
1t8sA02
A:173-484
2b
1t8sC02
C:173-484
2c
1t8sD02
D:173-484
2d
1t8sE02
E:173-484
2e
1t8sF02
F:173-484
2f
1t8sB02
B:173-484
[
close CATH info
]
Pfam Domains
(2, 12)
Info
all PFAM domains
1a: PFAM_PNP_UDP_1_1t8sF01 (F:229-452)
1b: PFAM_PNP_UDP_1_1t8sF02 (F:229-452)
1c: PFAM_PNP_UDP_1_1t8sF03 (F:229-452)
1d: PFAM_PNP_UDP_1_1t8sF04 (F:229-452)
1e: PFAM_PNP_UDP_1_1t8sF05 (F:229-452)
1f: PFAM_PNP_UDP_1_1t8sF06 (F:229-452)
2a: PFAM_AMNp_N_1t8sF07 (F:11-172)
2b: PFAM_AMNp_N_1t8sF08 (F:11-172)
2c: PFAM_AMNp_N_1t8sF09 (F:11-172)
2d: PFAM_AMNp_N_1t8sF10 (F:11-172)
2e: PFAM_AMNp_N_1t8sF11 (F:11-172)
2f: PFAM_AMNp_N_1t8sF12 (F:11-172)
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Clans
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)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
PUP
(121)
Family
:
PNP_UDP_1
(121)
Escherichia coli O157:H7
(16)
1a
PNP_UDP_1-1t8sF01
F:229-452
1b
PNP_UDP_1-1t8sF02
F:229-452
1c
PNP_UDP_1-1t8sF03
F:229-452
1d
PNP_UDP_1-1t8sF04
F:229-452
1e
PNP_UDP_1-1t8sF05
F:229-452
1f
PNP_UDP_1-1t8sF06
F:229-452
Clan
:
no clan defined [family: AMNp_N]
(4)
Family
:
AMNp_N
(4)
Escherichia coli O157:H7
(4)
2a
AMNp_N-1t8sF07
F:11-172
2b
AMNp_N-1t8sF08
F:11-172
2c
AMNp_N-1t8sF09
F:11-172
2d
AMNp_N-1t8sF10
F:11-172
2e
AMNp_N-1t8sF11
F:11-172
2f
AMNp_N-1t8sF12
F:11-172
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