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1ND5
Biol. Unit 1
Info
Asym.Unit (247 KB)
Biol.Unit 1 (180 KB)
Biol.Unit 2 (121 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
:
2.90
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
[
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Hetero Components
(4, 19)
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
7
Ligand/Ion
PENTAETHYLENE GLYCOL
2
2BF
3
Ligand/Ion
ALPHA-BENZYL-AMINOBENZYL-PHOSPHONIC ACID
3
MAN
-1
Ligand/Ion
ALPHA-D-MANNOSE
4
NAG
8
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
5
NDG
1
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
[
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Sites
(22, 22)
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: BC3 (SOFTWARE)
11: BC4 (SOFTWARE)
12: BC5 (SOFTWARE)
13: BC6 (SOFTWARE)
14: BC7 (SOFTWARE)
15: BC8 (SOFTWARE)
16: BC9 (SOFTWARE)
17: CC1 (SOFTWARE)
18: CC2 (SOFTWARE)
19: CC4 (SOFTWARE)
20: CC5 (SOFTWARE)
21: CC6 (SOFTWARE)
22: CC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
VAL A:186 , HIS A:187 , ASN A:188 , HOH A:4117 , NAG A:5001
BINDING SITE FOR RESIDUE NAG A 5000
02
AC2
SOFTWARE
NAG A:5000
BINDING SITE FOR RESIDUE NAG A 5001
03
AC3
SOFTWARE
ASN A:272 , LEU A:274 , PRO A:277 , ASN A:301 , GLU A:302 , TYR A:308 , NAG A:5003
BINDING SITE FOR RESIDUE NAG A 5002
04
AC4
SOFTWARE
NAG A:5002
BINDING SITE FOR RESIDUE NAG A 5003
05
AC5
SOFTWARE
VAL B:1184 , HIS B:1185 , ASN B:1186 , HOH B:4044
BINDING SITE FOR RESIDUE NDG B 5004
06
AC6
SOFTWARE
ASN B:1270 , LEU B:1272 , PRO B:1275 , ASN B:1299 , GLU B:1300 , TYR B:1306 , NAG B:5006
BINDING SITE FOR RESIDUE NAG B 5005
07
AC7
SOFTWARE
NAG B:5005
BINDING SITE FOR RESIDUE NAG B 5006
08
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
09
AC9
SOFTWARE
NAG C:5007
BINDING SITE FOR RESIDUE NAG C 5008
10
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
11
BC4
SOFTWARE
GLU B:1290 , GLU B:1320 , NAG D:5011
BINDING SITE FOR RESIDUE MAN D 5012
12
BC5
SOFTWARE
ARG A:11 , HIS A:12 , ARG A:15 , ILE A:18 , ARG A:79 , TYR A:123 , PHE A:171 , SER A:175 , HIS A:257 , ASP A:258 , THR A:259 , 1PE A:7004
BINDING SITE FOR RESIDUE 2BF A 6000
13
BC6
SOFTWARE
ARG B:1010 , HIS B:1011 , ARG B:1014 , ILE B:1017 , ARG B:1078 , TYR B:1122 , PHE B:1169 , SER B:1173 , HIS B:1255 , ASP B:1256 , THR B:1257 , 1PE B:7005
BINDING SITE FOR RESIDUE 2BF B 6001
14
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
15
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
16
BC9
SOFTWARE
SER A:117 , ASP A:119 , GLN A:120 , PHE A:126 , ASN A:128 , TRP A:336
BINDING SITE FOR RESIDUE 1PE A 7000
17
CC1
SOFTWARE
SER B:1116 , GLN B:1119 , ASN B:1127 , TRP B:1334
BINDING SITE FOR RESIDUE 1PE B 7001
18
CC2
SOFTWARE
GLN C:2119 , PHE C:2125 , ASN C:2127 , TRP C:2335
BINDING SITE FOR RESIDUE 1PE C 7002
19
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
20
CC5
SOFTWARE
TYR B:1122 , PRO B:1124 , ARG B:1126 , PHE B:1169 , 2BF B:6001
BINDING SITE FOR RESIDUE 1PE B 7005
21
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
22
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, 12)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_047961 (F3091V, chain A/B/C/A/B/C, )
2: VAR_047962 (W3193R, chain A/B/C/A/B/C, )
3: VAR_047963 (Y3297H, chain A/B/C/A/B/C, )
4: VAR_047964 (V3327A, chain A/B/C/A/B/C, )
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
F
92
1091
2091
3091
V
2
UniProt
VAR_047962
W
226
R
PPAP_HUMAN
Polymorphism
17856253
A
B
C
A/B/C
W
194
1192
2193
3193
R
3
UniProt
VAR_047963
Y
330
H
PPAP_HUMAN
Polymorphism
17851392
A
B
C
A/B/C
Y
298
1296
2297
3297
H
4
UniProt
VAR_047964
V
360
A
PPAP_HUMAN
Polymorphism
17850198
A
B
C
A/B/C
V
328
1326
2327
3327
A
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(2, 6)
Info
All PROSITE Patterns/Profiles
1: HIS_ACID_PHOSPHAT_1 (A:3-17,B:1002-1016,C:2002-2016)
2: HIS_ACID_PHOSPHAT_2 (A:251-267,B:1249-1265,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
3
A:3-17
B:1002-1016
C:2002-2016
-
2
HIS_ACID_PHOSPHAT_2
PS00778
Histidine acid phosphatases active site signature.
PPAP_HUMAN
283-299
3
A:251-267
B:1249-1265
C:2250-2266
-
[
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Exons
(0, 0)
Info
All Exons
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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_d1nd5a_ (A:)
1b: SCOP_d1nd5b_ (B:)
1c: SCOP_d1nd5c_ (C:)
1d: SCOP_d1nd5d_ (D:)
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Protein Domains
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)
Organisms
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)
(
)
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
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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)
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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
1nd5A00
A:1-342
1b
1nd5B00
B:1000-1341
1c
1nd5C00
C:2000-2341
1d
1nd5D00
D:3000-3341
[
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]
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)
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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
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Asymmetric Unit 1
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