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1ND6
Biol. Unit 3
Info
Asym.Unit (254 KB)
Biol.Unit 1 (127 KB)
Biol.Unit 2 (124 KB)
Biol.Unit 3 (246 KB)
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(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
:
2.40
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: A,B,C,D (1x)
Keywords
:
Prostatic 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
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Hetero Components
(5, 30)
Info
All Hetero Components
1a: PENTAETHYLENE GLYCOL (1PEa)
1b: PENTAETHYLENE GLYCOL (1PEb)
1c: PENTAETHYLENE GLYCOL (1PEc)
1d: PENTAETHYLENE GLYCOL (1PEd)
2a: GLYCINE (GLYa)
3a: ALPHA-D-MANNOSE (MANa)
3b: ALPHA-D-MANNOSE (MANb)
3c: ALPHA-D-MANNOSE (MANc)
3d: ALPHA-D-MANNOSE (MANd)
3e: ALPHA-D-MANNOSE (MANe)
3f: ALPHA-D-MANNOSE (MANf)
3g: ALPHA-D-MANNOSE (MANg)
3h: ALPHA-D-MANNOSE (MANh)
3i: ALPHA-D-MANNOSE (MANi)
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)
4l: N-ACETYL-D-GLUCOSAMINE (NAGl)
5a: PHOSPHATE ION (PO4a)
5b: PHOSPHATE ION (PO4b)
5c: PHOSPHATE ION (PO4c)
5d: PHOSPHATE ION (PO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1PE
4
Ligand/Ion
PENTAETHYLENE GLYCOL
2
GLY
1
Mod. Amino Acid
GLYCINE
3
MAN
9
Ligand/Ion
ALPHA-D-MANNOSE
4
NAG
12
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
5
PO4
4
Ligand/Ion
PHOSPHATE ION
[
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Sites
(30, 30)
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)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
VAL A:186 , HIS A:187 , ASN A:188 , NAG A:5001
BINDING SITE FOR RESIDUE NAG A 5000
02
AC2
SOFTWARE
NAG A:5000 , MAN A:5002
BINDING SITE FOR RESIDUE NAG A 5001
03
AC3
SOFTWARE
NAG A:5001 , MAN A:5003
BINDING SITE FOR RESIDUE MAN A 5002
04
AC4
SOFTWARE
MAN A:5002
BINDING SITE FOR RESIDUE MAN A 5003
05
AC5
SOFTWARE
ASN A:272 , LEU A:274 , ASN A:301 , GLU A:302 , TYR A:308 , NAG A:5005
BINDING SITE FOR RESIDUE NAG A 5004
06
AC6
SOFTWARE
NAG A:5004
BINDING SITE FOR RESIDUE NAG A 5005
07
AC7
SOFTWARE
VAL B:1185 , HIS B:1186 , ASN B:1187
BINDING SITE FOR RESIDUE NAG B 5006
08
AC8
SOFTWARE
ASN B:1271 , LEU B:1273 , ASN B:1300 , GLU B:1301 , TYR B:1307 , HOH B:4176 , HOH B:4177 , NAG B:5008
BINDING SITE FOR RESIDUE NAG B 5007
09
AC9
SOFTWARE
ASN B:1271 , NAG B:5007 , MAN B:5009
BINDING SITE FOR RESIDUE NAG B 5008
10
BC1
SOFTWARE
NAG B:5008 , MAN B:5010 , MAN B:5011
BINDING SITE FOR RESIDUE MAN B 5009
11
BC2
SOFTWARE
MAN B:5009 , GLU D:3288
BINDING SITE FOR RESIDUE MAN B 5010
12
BC3
SOFTWARE
HOH B:4414 , MAN B:5009 , LYS D:3000
BINDING SITE FOR RESIDUE MAN B 5011
13
BC4
SOFTWARE
ASN C:2271 , LEU C:2273 , ASN C:2300 , GLU C:2301 , TYR C:2307 , NAG C:5013
BINDING SITE FOR RESIDUE NAG C 5012
14
BC5
SOFTWARE
TYR C:2307 , NAG C:5012 , MAN C:5014
BINDING SITE FOR RESIDUE NAG C 5013
15
BC6
SOFTWARE
NAG C:5013 , GLN D:3333
BINDING SITE FOR RESIDUE MAN C 5014
16
BC7
SOFTWARE
VAL D:3185 , ASN D:3187
BINDING SITE FOR RESIDUE NAG D 5015
17
BC8
SOFTWARE
ASN D:3271 , LEU D:3273 , ASN D:3300 , GLU D:3301 , TYR D:3307 , NAG D:5017
BINDING SITE FOR RESIDUE NAG D 5016
18
BC9
SOFTWARE
GLY B:1313 , CYS B:1314 , SER B:1315 , TYR D:3307 , NAG D:5016 , MAN D:5018
BINDING SITE FOR RESIDUE NAG D 5017
19
CC1
SOFTWARE
GLU B:1291 , NAG D:5017 , MAN D:5019 , MAN D:5020
BINDING SITE FOR RESIDUE MAN D 5018
20
CC2
SOFTWARE
GLU B:1321 , MAN D:5018 , MAN D:5020
BINDING SITE FOR RESIDUE MAN D 5019
21
CC3
SOFTWARE
ARG B:1322 , GLU B:1325 , MAN D:5018 , MAN D:5019
BINDING SITE FOR RESIDUE MAN D 5020
22
CC4
SOFTWARE
ARG A:11 , HIS A:12 , ARG A:15 , ARG A:79 , HIS A:257 , ASP A:258
BINDING SITE FOR RESIDUE PO4 A 8000
23
CC5
SOFTWARE
ARG B:1010 , HIS B:1011 , ARG B:1014 , ARG B:1078 , HIS B:1256 , ASP B:1257
BINDING SITE FOR RESIDUE PO4 B 8001
24
CC6
SOFTWARE
ARG C:2010 , HIS C:2011 , ARG C:2014 , ARG C:2078 , HIS C:2256 , ASP C:2257
BINDING SITE FOR RESIDUE PO4 C 8002
25
CC7
SOFTWARE
ARG D:3010 , HIS D:3011 , ARG D:3014 , ARG D:3078 , HIS D:3256 , ASP D:3257
BINDING SITE FOR RESIDUE PO4 D 8003
26
CC8
SOFTWARE
HIS B:1304 , GLU B:1305 , TYR B:1307
BINDING SITE FOR RESIDUE GLY B 9000
27
CC9
SOFTWARE
SER A:117 , ASP A:119 , GLN A:120 , PHE A:126 , ASN A:128 , TRP A:336 , LYS D:3160
BINDING SITE FOR RESIDUE 1PE A 6000
28
DC1
SOFTWARE
SER B:1116 , GLN B:1119 , PHE B:1125 , ASN B:1127 , TRP B:1335 , HOH B:4444
BINDING SITE FOR RESIDUE 1PE B 7000
29
DC2
SOFTWARE
HOH A:4285 , SER C:2116 , ASP C:2118 , GLN C:2119 , PHE C:2125 , ASN C:2127 , TRP C:2335
BINDING SITE FOR RESIDUE 1PE C 7001
30
DC3
SOFTWARE
SER D:3116 , ASP D:3118 , GLN D:3119 , PHE D:3125 , ASN D:3127 , TRP D:3335 , HOH D:4439
BINDING SITE FOR RESIDUE 1PE D 7002
[
close Site info
]
SAPs(SNPs)/Variants
(4, 16)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_047961 (F3091V, chain A/B/C/A/B/C/D, )
2: VAR_047962 (W3193R, chain A/B/C/A/B/C/D, )
3: VAR_047963 (Y3297H, chain A/B/C/A/B/C/D, )
4: VAR_047964 (V3327A, chain A/B/C/A/B/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
A/B/C/D
F
92
1091
2091
3091
V
2
UniProt
VAR_047962
W
226
R
PPAP_HUMAN
Polymorphism
17856253
A
B
C
A/B/C/D
W
194
1193
2193
3193
R
3
UniProt
VAR_047963
Y
330
H
PPAP_HUMAN
Polymorphism
17851392
A
B
C
A/B/C/D
Y
298
1297
2297
3297
H
4
UniProt
VAR_047964
V
360
A
PPAP_HUMAN
Polymorphism
17850198
A
B
C
A/B/C/D
V
328
1327
2327
3327
A
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: HIS_ACID_PHOSPHAT_1 (A:3-17,B:1002-1016,C:2002-2016,D:3...)
2: HIS_ACID_PHOSPHAT_2 (A:251-267,B:1250-1266,C:2250-2266,...)
;
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
4
A:3-17
B:1002-1016
C:2002-2016
D:3002-3016
2
HIS_ACID_PHOSPHAT_2
PS00778
Histidine acid phosphatases active site signature.
PPAP_HUMAN
283-299
4
A:251-267
B:1250-1266
C:2250-2266
D:3250-3266
[
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Exons
(0, 0)
Info
All Exons
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1nd6a_ (A:)
1b: SCOP_d1nd6b_ (B:)
1c: SCOP_d1nd6c_ (C:)
1d: SCOP_d1nd6d_ (D:)
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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
d1nd6a_
A:
1b
d1nd6b_
B:
1c
d1nd6c_
C:
1d
d1nd6d_
D:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1nd6A00 (A:1-342)
1b: CATH_1nd6C00 (C:2000-2341)
1c: CATH_1nd6D00 (D:3000-3341)
1d: CATH_1nd6B00 (B:1000-1342)
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)
(
)
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(
)
(
)
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
1nd6A00
A:1-342
1b
1nd6C00
C:2000-2341
1c
1nd6D00
D:3000-3341
1d
1nd6B00
B:1000-1342
[
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]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_His_Phos_2_1nd6D01 (D:3001-3299)
1b: PFAM_His_Phos_2_1nd6D02 (D:3001-3299)
1c: PFAM_His_Phos_2_1nd6D03 (D:3001-3299)
1d: PFAM_His_Phos_2_1nd6D04 (D:3001-3299)
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Clan
:
PGM
(50)
Family
:
His_Phos_2
(19)
Homo sapiens (Human)
(5)
1a
His_Phos_2-1nd6D01
D:3001-3299
1b
His_Phos_2-1nd6D02
D:3001-3299
1c
His_Phos_2-1nd6D03
D:3001-3299
1d
His_Phos_2-1nd6D04
D:3001-3299
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