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...
Getting 'PROSITE' information from database.
1ND5
Biol. Unit 2
Info
Asym.Unit (247 KB)
Biol.Unit 1 (180 KB)
Biol.Unit 2 (121 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURES OF HUMAN PROSTATIC ACID PHOSPHATASE IN COMPLEX WITH A PHOSPHATE ION AND ALPHA-BENZYLAMINOBENZYLPHOSPHONIC ACID UPDATE THE MECHANISTIC PICTURE AND OFFER NEW INSIGHTS INTO INHIBITOR DESIGN
Authors
:
E. Ortlund, M. W. Lacount, L. Lebioda
Date
:
07 Dec 02 (Deposition) - 20 Dec 02 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Acid Phosphatase, Pap, Prostate, Phosphate, Inhibitor, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Ortlund, M. W. Lacount, L. Lebioda
Crystal Structures Of Human Prostatic Acid Phosphatase In Complex With A Phosphate Ion And Alpha-Benzylaminobenzylphosphonic Acid Update The Mechanistic Picture And Offer New Insights Into Inhibitor Design
Biochemistry V. 42 383 2003
[
close entry info
]
Hetero Components
(4, 11)
Info
All Hetero Components
1a: PENTAETHYLENE GLYCOL (1PEa)
1b: PENTAETHYLENE GLYCOL (1PEb)
1c: PENTAETHYLENE GLYCOL (1PEc)
1d: PENTAETHYLENE GLYCOL (1PEd)
1e: PENTAETHYLENE GLYCOL (1PEe)
1f: PENTAETHYLENE GLYCOL (1PEf)
1g: PENTAETHYLENE GLYCOL (1PEg)
1h: PENTAETHYLENE GLYCOL (1PEh)
2a: ALPHA-BENZYL-AMINOBENZYL-PHOSPHONI... (2BFa)
2b: ALPHA-BENZYL-AMINOBENZYL-PHOSPHONI... (2BFb)
2c: ALPHA-BENZYL-AMINOBENZYL-PHOSPHONI... (2BFc)
2d: ALPHA-BENZYL-AMINOBENZYL-PHOSPHONI... (2BFd)
3a: ALPHA-D-MANNOSE (MANa)
4a: N-ACETYL-D-GLUCOSAMINE (NAGa)
4b: N-ACETYL-D-GLUCOSAMINE (NAGb)
4c: N-ACETYL-D-GLUCOSAMINE (NAGc)
4d: N-ACETYL-D-GLUCOSAMINE (NAGd)
4e: N-ACETYL-D-GLUCOSAMINE (NAGe)
4f: N-ACETYL-D-GLUCOSAMINE (NAGf)
4g: N-ACETYL-D-GLUCOSAMINE (NAGg)
4h: N-ACETYL-D-GLUCOSAMINE (NAGh)
4i: N-ACETYL-D-GLUCOSAMINE (NAGi)
4j: N-ACETYL-D-GLUCOSAMINE (NAGj)
4k: N-ACETYL-D-GLUCOSAMINE (NAGk)
5a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1PE
3
Ligand/Ion
PENTAETHYLENE GLYCOL
2
2BF
2
Ligand/Ion
ALPHA-BENZYL-AMINOBENZYL-PHOSPHONIC ACID
3
MAN
1
Ligand/Ion
ALPHA-D-MANNOSE
4
NAG
5
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
5
NDG
-1
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
[
close Hetero Component info
]
Sites
(13, 13)
Info
All Sites
01: AC8 (SOFTWARE)
02: AC9 (SOFTWARE)
03: BC1 (SOFTWARE)
04: BC2 (SOFTWARE)
05: BC3 (SOFTWARE)
06: BC4 (SOFTWARE)
07: BC7 (SOFTWARE)
08: BC8 (SOFTWARE)
09: CC2 (SOFTWARE)
10: CC3 (SOFTWARE)
11: CC4 (SOFTWARE)
12: CC6 (SOFTWARE)
13: CC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC8
SOFTWARE
ASN C:2271 , LEU C:2273 , ASN C:2300 , GLU C:2301 , TYR C:2307 , NAG C:5008
BINDING SITE FOR RESIDUE NAG C 5007
02
AC9
SOFTWARE
NAG C:5007
BINDING SITE FOR RESIDUE NAG C 5008
03
BC1
SOFTWARE
VAL D:3185 , HIS D:3186 , ASN D:3187
BINDING SITE FOR RESIDUE NAG D 5009
04
BC2
SOFTWARE
ASN D:3271 , LEU D:3273 , ASN D:3300 , GLU D:3301 , TYR D:3307 , NAG D:5011
BINDING SITE FOR RESIDUE NAG D 5010
05
BC3
SOFTWARE
CYS B:1313 , SER B:1314 , ARG B:1321 , TYR D:3307 , NAG D:5010 , MAN D:5012
BINDING SITE FOR RESIDUE NAG D 5011
06
BC4
SOFTWARE
GLU B:1290 , GLU B:1320 , NAG D:5011
BINDING SITE FOR RESIDUE MAN D 5012
07
BC7
SOFTWARE
ARG C:2010 , HIS C:2011 , ARG C:2014 , ILE C:2017 , ARG C:2078 , TYR C:2122 , PHE C:2170 , SER C:2174 , HIS C:2256 , ASP C:2257 , THR C:2258 , 1PE C:7006
BINDING SITE FOR RESIDUE 2BF C 6002
08
BC8
SOFTWARE
1PE A:7007 , ARG D:3010 , HIS D:3011 , ARG D:3014 , ILE D:3017 , ARG D:3078 , TYR D:3122 , SER D:3174 , ASP D:3178 , HIS D:3256 , ASP D:3257 , THR D:3258
BINDING SITE FOR RESIDUE 2BF D 6003
09
CC2
SOFTWARE
GLN C:2119 , PHE C:2125 , ASN C:2127 , TRP C:2335
BINDING SITE FOR RESIDUE 1PE C 7002
10
CC3
SOFTWARE
GLN D:3119 , PHE D:3125 , ASN D:3127 , TRP D:3335 , HOH D:4102
BINDING SITE FOR RESIDUE 1PE D 7003
11
CC4
SOFTWARE
TYR A:123 , PRO A:125 , ARG A:127 , PHE A:171 , LEU A:214 , 2BF A:6000 , HIS D:3165
BINDING SITE FOR RESIDUE 1PE A 7004
12
CC6
SOFTWARE
LYS B:1159 , HIS B:1164 , TYR C:2122 , LEU C:2123 , PRO C:2124 , ARG C:2126 , GLU C:2135 , PHE C:2170 , SER C:2209 , 2BF C:6002
BINDING SITE FOR RESIDUE 1PE C 7006
13
CC7
SOFTWARE
LYS A:176 , ARG D:3126 , PHE D:3170 , 2BF D:6003
BINDING SITE FOR RESIDUE 1PE A 7007
[
close Site info
]
SAPs(SNPs)/Variants
(4, 8)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_047961 (F3091V, chain A/B/C/C/D, )
2: VAR_047962 (W3193R, chain A/B/C/C/D, )
3: VAR_047963 (Y3297H, chain A/B/C/C/D, )
4: VAR_047964 (V3327A, chain A/B/C/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_047961
F
124
V
PPAP_HUMAN
Polymorphism
17856254
A
B
C
C/D
F
92
1091
2091
3091
V
2
UniProt
VAR_047962
W
226
R
PPAP_HUMAN
Polymorphism
17856253
A
B
C
C/D
W
194
1192
2193
3193
R
3
UniProt
VAR_047963
Y
330
H
PPAP_HUMAN
Polymorphism
17851392
A
B
C
C/D
Y
298
1296
2297
3297
H
4
UniProt
VAR_047964
V
360
A
PPAP_HUMAN
Polymorphism
17850198
A
B
C
C/D
V
328
1326
2327
3327
A
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: HIS_ACID_PHOSPHAT_1 (C:2002-2016,D:3002-3016)
2: HIS_ACID_PHOSPHAT_2 (C:2250-2266,D:3250-3266)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
HIS_ACID_PHOSPHAT_1
PS00616
Histidine acid phosphatases phosphohistidine signature.
PPAP_HUMAN
35-49
2
-
-
C:2002-2016
D:3002-3016
2
HIS_ACID_PHOSPHAT_2
PS00778
Histidine acid phosphatases active site signature.
PPAP_HUMAN
283-299
2
-
-
C:2250-2266
D:3250-3266
[
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1nd5a_ (A:)
1b: SCOP_d1nd5b_ (B:)
1c: SCOP_d1nd5c_ (C:)
1d: SCOP_d1nd5d_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Phosphoglycerate mutase-like
(103)
Superfamily
:
Phosphoglycerate mutase-like
(103)
Family
:
Histidine acid phosphatase
(24)
Protein domain
:
Prostatic acid phosphatase
(6)
Human (Homo sapiens) [TaxId: 9606]
(4)
1a
d1nd5a_
A:
1b
d1nd5b_
B:
1c
d1nd5c_
C:
1d
d1nd5d_
D:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1nd5A00 (A:1-342)
1b: CATH_1nd5B00 (B:1000-1341)
1c: CATH_1nd5C00 (C:2000-2341)
1d: CATH_1nd5D00 (D:3000-3341)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Phosphoglycerate mutase-like
(91)
Human (Homo sapiens)
(18)
1a
1nd5A00
A:1-342
1b
1nd5B00
B:1000-1341
1c
1nd5C00
C:2000-2341
1d
1nd5D00
D:3000-3341
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_His_Phos_2_1nd5D01 (D:3001-3299)
1b: PFAM_His_Phos_2_1nd5D02 (D:3001-3299)
1c: PFAM_His_Phos_2_1nd5D03 (D:3001-3299)
1d: PFAM_His_Phos_2_1nd5D04 (D:3001-3299)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
PGM
(50)
Family
:
His_Phos_2
(19)
Homo sapiens (Human)
(5)
1a
His_Phos_2-1nd5D01
D:3001-3299
1b
His_Phos_2-1nd5D02
D:3001-3299
1c
His_Phos_2-1nd5D03
D:3001-3299
1d
His_Phos_2-1nd5D04
D:3001-3299
[
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 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 (247 KB)
Header - Asym.Unit
Biol.Unit 1 (180 KB)
Header - Biol.Unit 1
Biol.Unit 2 (121 KB)
Header - Biol.Unit 2
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
1ND5
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help