PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
1HPU
Asym. Unit
Info
Asym.Unit (363 KB)
Biol.Unit 1 (94 KB)
Biol.Unit 2 (95 KB)
Biol.Unit 3 (95 KB)
Biol.Unit 4 (95 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
5'-NUCLEOTIDASE (CLOSED FORM), COMPLEX WITH AMPCP
Authors
:
T. Knoefel, N. Straeter
Date
:
13 Dec 00 (Deposition) - 20 Mar 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.85
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
:
Metalloenzyme, Metallophosphatase, Domain Rotation, Domain Movement, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Knofel, N. Strater
Mechanism Of Hydrolysis Of Phosphate Esters By The Dimetal Center Of 5'-Nucleotidase Based On Crystal Structures.
J. Mol. Biol. V. 309 239 2001
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 12)
Info
All Hetero Components
1a: PHOSPHOMETHYLPHOSPHONIC ACID ADENO... (A12a)
1b: PHOSPHOMETHYLPHOSPHONIC ACID ADENO... (A12b)
1c: PHOSPHOMETHYLPHOSPHONIC ACID ADENO... (A12c)
1d: PHOSPHOMETHYLPHOSPHONIC ACID ADENO... (A12d)
2a: MANGANESE (II) ION (MNa)
2b: MANGANESE (II) ION (MNb)
2c: MANGANESE (II) ION (MNc)
2d: MANGANESE (II) ION (MNd)
2e: MANGANESE (II) ION (MNe)
2f: MANGANESE (II) ION (MNf)
2g: MANGANESE (II) ION (MNg)
2h: MANGANESE (II) ION (MNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
A12
4
Ligand/Ion
PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2
MN
8
Ligand/Ion
MANGANESE (II) ION
[
close Hetero Component info
]
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
ASP A:84 , ASN A:116 , HIS A:217 , HIS A:252 , MN A:601 , A12 A:1602 , HOH A:1669
BINDING SITE FOR RESIDUE MN A 600
02
AC2
SOFTWARE
ASP A:41 , HIS A:43 , ASP A:84 , GLN A:254 , MN A:600 , A12 A:1602 , HOH A:1669
BINDING SITE FOR RESIDUE MN A 601
03
AC3
SOFTWARE
ASP B:84 , ASN B:116 , HIS B:217 , HIS B:252 , MN B:601 , A12 B:1603 , HOH B:1690
BINDING SITE FOR RESIDUE MN B 600
04
AC4
SOFTWARE
ASP B:41 , HIS B:43 , ASP B:84 , GLN B:254 , MN B:600 , A12 B:1603 , HOH B:1690
BINDING SITE FOR RESIDUE MN B 601
05
AC5
SOFTWARE
ASP C:84 , ASN C:116 , HIS C:217 , HIS C:252 , MN C:601 , A12 C:1604 , HOH C:1681
BINDING SITE FOR RESIDUE MN C 600
06
AC6
SOFTWARE
ASP C:41 , HIS C:43 , ASP C:84 , GLN C:254 , MN C:600 , HOH C:1681 , HOH C:1885
BINDING SITE FOR RESIDUE MN C 601
07
AC7
SOFTWARE
ASP D:84 , ASN D:116 , HIS D:217 , HIS D:252 , MN D:601 , A12 D:1605 , HOH D:1652
BINDING SITE FOR RESIDUE MN D 600
08
AC8
SOFTWARE
ASP D:41 , HIS D:43 , ASP D:84 , GLN D:254 , MN D:600 , HOH D:1652 , HOH D:1812
BINDING SITE FOR RESIDUE MN D 601
09
AC9
SOFTWARE
ASP A:84 , ASN A:116 , HIS A:117 , ASP A:120 , ILE A:178 , HIS A:252 , GLN A:254 , ARG A:375 , ARG A:379 , SER A:405 , GLY A:407 , ARG A:410 , PHE A:429 , ASN A:431 , GLY A:458 , PHE A:498 , ASP A:504 , MN A:600 , MN A:601 , HOH A:1631 , HOH A:1633 , HOH A:1669 , HOH A:1673 , HOH A:1742
BINDING SITE FOR RESIDUE A12 A 1602
10
BC1
SOFTWARE
ASP B:84 , ASN B:116 , HIS B:117 , ASP B:120 , ILE B:178 , HIS B:252 , GLN B:254 , ARG B:375 , ARG B:379 , SER B:405 , GLY B:407 , ARG B:410 , PHE B:429 , ASN B:431 , GLY B:458 , PHE B:498 , ASP B:504 , MN B:600 , MN B:601 , HOH B:1690 , HOH B:1702 , HOH B:1719 , HOH B:1738 , HOH B:1768 , HOH B:1905
BINDING SITE FOR RESIDUE A12 B 1603
11
BC2
SOFTWARE
ASP C:84 , ASN C:116 , HIS C:117 , ILE C:178 , HIS C:252 , ARG C:375 , ARG C:379 , SER C:405 , GLY C:407 , ARG C:410 , PHE C:429 , ASN C:431 , GLY C:458 , PHE C:498 , ASP C:504 , MN C:600 , HOH C:1679 , HOH C:1681 , HOH C:1693 , HOH C:1795 , HOH C:1797 , HOH C:1808 , HOH C:1885
BINDING SITE FOR RESIDUE A12 C 1604
12
BC3
SOFTWARE
ASP D:84 , ASN D:116 , HIS D:117 , ILE D:178 , HIS D:252 , ARG D:375 , ARG D:379 , SER D:405 , GLY D:407 , ARG D:410 , PHE D:429 , ASN D:431 , GLY D:458 , PHE D:498 , ASP D:504 , MN D:600 , HOH D:1652 , HOH D:1771 , HOH D:1812 , HOH D:1824 , HOH D:1835 , HOH D:1864
BINDING SITE FOR RESIDUE A12 D 1605
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: 5_NUCLEOTIDASE_1 (A:34-46,B:34-46,C:34-46,D:34-46)
2: 5_NUCLEOTIDASE_2 (A:109-120,B:109-120,C:109-120,D:10...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
5_NUCLEOTIDASE_1
PS00785
5'-nucleotidase signature 1.
USHA_ECOLI
34-46
4
A:34-46
B:34-46
C:34-46
D:34-46
2
5_NUCLEOTIDASE_2
PS00786
5'-nucleotidase signature 2.
USHA_ECOLI
109-120
4
A:109-120
B:109-120
C:109-120
D:109-120
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1hpua1 (A:363-550)
1b: SCOP_d1hpub1 (B:363-550)
1c: SCOP_d1hpuc1 (C:363-550)
1d: SCOP_d1hpud1 (D:363-550)
2a: SCOP_d1hpua2 (A:26-362)
2b: SCOP_d1hpub2 (B:26-362)
2c: SCOP_d1hpuc2 (C:26-362)
2d: SCOP_d1hpud2 (D:26-362)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain
(10)
Superfamily
:
5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain
(10)
Family
:
5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain
(10)
Protein domain
:
5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain
(10)
Escherichia coli [TaxId: 562]
(8)
1a
d1hpua1
A:363-550
1b
d1hpub1
B:363-550
1c
d1hpuc1
C:363-550
1d
d1hpud1
D:363-550
Fold
:
Metallo-dependent phosphatases
(115)
Superfamily
:
Metallo-dependent phosphatases
(115)
Family
:
5'-nucleotidase (syn. UDP-sugar hydrolase), N-terminal domain
(10)
Protein domain
:
5'-nucleotidase (syn. UDP-sugar hydrolase), N-terminal domain
(10)
Escherichia coli [TaxId: 562]
(8)
2a
d1hpua2
A:26-362
2b
d1hpub2
B:26-362
2c
d1hpuc2
C:26-362
2d
d1hpud2
D:26-362
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1hpuA01 (A:26-362)
1b: CATH_1hpuB01 (B:26-362)
1c: CATH_1hpuC01 (C:26-362)
1d: CATH_1hpuD01 (D:26-362)
2a: CATH_1hpuA02 (A:363-549)
2b: CATH_1hpuB02 (B:363-549)
2c: CATH_1hpuC02 (C:363-549)
2d: CATH_1hpuD02 (D:363-549)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
4-Layer Sandwich
(459)
Topology
:
Purple Acid Phosphatase; chain A, domain 2
(87)
Homologous Superfamily
:
[code=3.60.21.10, no name defined]
(83)
Escherichia coli. Organism_taxid: 562.
(4)
1a
1hpuA01
A:26-362
1b
1hpuB01
B:26-362
1c
1hpuC01
C:26-362
1d
1hpuD01
D:26-362
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
5'-nucleotidase; domain 2
(9)
Homologous Superfamily
:
5'-nucleotidase; Domain 2
(9)
Escherichia coli. Organism_taxid: 562.
(3)
2a
1hpuA02
A:363-549
2b
1hpuB02
B:363-549
2c
1hpuC02
C:363-549
2d
1hpuD02
D:363-549
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (363 KB)
Header - Asym.Unit
Biol.Unit 1 (94 KB)
Header - Biol.Unit 1
Biol.Unit 2 (95 KB)
Header - Biol.Unit 2
Biol.Unit 3 (95 KB)
Header - Biol.Unit 3
Biol.Unit 4 (95 KB)
Header - Biol.Unit 4
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
1HPU
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
