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2QFP
Biol. Unit 2
Info
Asym.Unit (306 KB)
Biol.Unit 1 (153 KB)
Biol.Unit 2 (151 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF RED KIDNEY BEAN PURPLE ACID PHOSPHATASE IN COMPLEX WITH FLUORIDE
Authors
:
L. W. Guddat, G. S. Schenk, L. R. Gahan, T. W. Elliot, E. Leung
Date
:
27 Jun 07 (Deposition) - 14 Oct 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Binuclear, Fe-Zn, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. Schenk, T. W. Elliott, E. Leung, L. E. Carrington, N. Mitic, L. R. Gahan, L. W. Guddat
Crystal Structures Of A Purple Acid Phosphatase, Representing Different Steps Of This Enzyme'S Catalytic Cycle.
Bmc Struct. Biol. V. 8 6 2008
[
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Hetero Components
(3, 12)
Info
All Hetero Components
2a: FE (III) ION (FEa)
2b: FE (III) ION (FEb)
2c: FE (III) ION (FEc)
2d: FE (III) ION (FEd)
1a: FLUORIDE ION (Fa)
1b: FLUORIDE ION (Fb)
1c: FLUORIDE ION (Fc)
1d: FLUORIDE ION (Fd)
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)
4m: N-ACETYL-D-GLUCOSAMINE (NAGm)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
3c: SODIUM ION (NAc)
3d: SODIUM ION (NAd)
3e: SODIUM ION (NAe)
3f: SODIUM ION (NAf)
3g: SODIUM ION (NAg)
4h: SODIUM ION (NAh)
4i: SODIUM ION (NAi)
4j: SODIUM ION (NAj)
4k: SODIUM ION (NAk)
5a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
5b: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGb)
5c: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGc)
6a: SULFATE ION (SO4a)
6b: SULFATE ION (SO4b)
6c: SULFATE ION (SO4c)
6d: SULFATE ION (SO4d)
6e: SULFATE ION (SO4e)
6f: SULFATE ION (SO4f)
6g: SULFATE ION (SO4g)
6h: SULFATE ION (SO4h)
7a: ZINC ION (ZNa)
7b: ZINC ION (ZNb)
7c: ZINC ION (ZNc)
7d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
F
-1
Ligand/Ion
FLUORIDE ION
2
FE
-1
Ligand/Ion
FE (III) ION
3
NA
-1
Ligand/Ion
SODIUM ION
4
NAG
7
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
5
NDG
1
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
6
SO4
4
Ligand/Ion
SULFATE ION
7
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(25, 25)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC5 (SOFTWARE)
03: AC9 (SOFTWARE)
04: BC1 (SOFTWARE)
05: BC2 (SOFTWARE)
06: BC3 (SOFTWARE)
07: BC4 (SOFTWARE)
08: BC5 (SOFTWARE)
09: BC6 (SOFTWARE)
10: BC7 (SOFTWARE)
11: DC6 (SOFTWARE)
12: DC7 (SOFTWARE)
13: DC8 (SOFTWARE)
14: DC9 (SOFTWARE)
15: EC1 (SOFTWARE)
16: EC2 (SOFTWARE)
17: EC3 (SOFTWARE)
18: EC4 (SOFTWARE)
19: EC5 (SOFTWARE)
20: EC6 (SOFTWARE)
21: EC7 (SOFTWARE)
22: EC8 (SOFTWARE)
23: EC9 (SOFTWARE)
24: FC1 (SOFTWARE)
25: FC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:81 , TYR D:24
BINDING SITE FOR RESIDUE NAG A 437
02
AC5
SOFTWARE
ASN B:81 , ASN B:173 , TYR C:24
BINDING SITE FOR RESIDUE NAG B 437
03
AC9
SOFTWARE
TYR B:24 , ASP B:50 , ASN C:81
BINDING SITE FOR RESIDUE NAG C 437
04
BC1
SOFTWARE
MET C:11 , ASP C:16 , PHE C:140 , ASN C:143 , SER C:147 , GLU C:150 , ARG C:188
BINDING SITE FOR RESIDUE NAG C 438
05
BC2
SOFTWARE
ASN C:396 , HIS C:399 , TRP C:419
BINDING SITE FOR RESIDUE NDG C 439
06
BC3
SOFTWARE
GLU C:51 , ARG C:108 , ASN C:109
BINDING SITE FOR RESIDUE NAG C 440
07
BC4
SOFTWARE
TYR A:24 , ASN D:81 , ASN D:173
BINDING SITE FOR RESIDUE NAG D 437
08
BC5
SOFTWARE
ASP D:16 , PHE D:140 , ASN D:143 , SER D:147
BINDING SITE FOR RESIDUE NAG D 438
09
BC6
SOFTWARE
LYS D:395 , ASN D:396
BINDING SITE FOR RESIDUE NAG D 439
10
BC7
SOFTWARE
ARG D:108 , ASN D:109
BINDING SITE FOR RESIDUE NAG D 440
11
DC6
SOFTWARE
ASP C:135 , ASP C:164 , TYR C:167 , HIS C:325 , ZN C:434 , SO4 C:435 , F C:436
BINDING SITE FOR RESIDUE FE C 433
12
DC7
SOFTWARE
ASP C:164 , ASN C:201 , HIS C:286 , HIS C:323 , FE C:433 , F C:436
BINDING SITE FOR RESIDUE ZN C 434
13
DC8
SOFTWARE
HIS C:202 , HIS C:295 , HIS C:325 , TYR C:365 , FE C:433 , F C:436 , NA C:443 , NA C:444 , SO4 D:441
BINDING SITE FOR RESIDUE SO4 C 435
14
DC9
SOFTWARE
ASP C:164 , ASN C:201 , HIS C:202 , HIS C:286 , HIS C:323 , FE C:433 , ZN C:434 , SO4 C:435 , NA C:443
BINDING SITE FOR RESIDUE F C 436
15
EC1
SOFTWARE
HIS C:296 , SO4 C:435 , NA C:442 , NA C:444 , ARG D:258 , HOH D:564
BINDING SITE FOR RESIDUE SO4 D 441
16
EC2
SOFTWARE
HIS C:295 , NA C:444 , SO4 D:441
BINDING SITE FOR RESIDUE NA C 442
17
EC3
SOFTWARE
ASN C:201 , HIS C:296 , SO4 C:435 , F C:436
BINDING SITE FOR RESIDUE NA C 443
18
EC4
SOFTWARE
HIS C:295 , SO4 C:435 , NA C:442 , SO4 D:441
BINDING SITE FOR RESIDUE NA C 444
19
EC5
SOFTWARE
ASP D:135 , ASP D:164 , TYR D:167 , HIS D:325 , ZN D:434 , F D:436
BINDING SITE FOR RESIDUE FE D 433
20
EC6
SOFTWARE
ASP D:135 , ASP D:164 , ASN D:201 , HIS D:286 , HIS D:323 , FE D:433 , F D:436
BINDING SITE FOR RESIDUE ZN D 434
21
EC7
SOFTWARE
SO4 C:441 , HIS D:202 , HIS D:295 , HIS D:325 , TYR D:365 , F D:436 , NA D:443
BINDING SITE FOR RESIDUE SO4 D 435
22
EC8
SOFTWARE
ASP D:164 , ASN D:201 , HIS D:323 , FE D:433 , ZN D:434 , SO4 D:435 , NA D:443
BINDING SITE FOR RESIDUE F D 436
23
EC9
SOFTWARE
ARG C:258 , HOH C:549 , HIS D:296 , SO4 D:435 , NA D:442 , NA D:443
BINDING SITE FOR RESIDUE SO4 C 441
24
FC1
SOFTWARE
SO4 C:441 , HIS D:295
BINDING SITE FOR RESIDUE NA D 442
25
FC2
SOFTWARE
SO4 C:441 , ASN D:201 , HIS D:296 , SO4 D:435 , F D:436
BINDING SITE FOR RESIDUE NA D 443
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
All Exons
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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
(2, 8)
Info
All SCOP Domains
1a: SCOP_d2qfpa1 (A:9-120)
1b: SCOP_d2qfpb1 (B:9-120)
1c: SCOP_d2qfpc1 (C:9-120)
1d: SCOP_d2qfpd1 (D:9-120)
2a: SCOP_d2qfpa2 (A:121-432)
2b: SCOP_d2qfpb2 (B:121-432)
2c: SCOP_d2qfpc2 (C:121-432)
2d: SCOP_d2qfpd2 (D:121-432)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Purple acid phosphatase, N-terminal domain
(9)
Family
:
automated matches
(5)
Protein domain
:
automated matches
(5)
French bean (Phaseolus vulgaris) [TaxId: 3885]
(5)
1a
d2qfpa1
A:9-120
1b
d2qfpb1
B:9-120
1c
d2qfpc1
C:9-120
1d
d2qfpd1
D:9-120
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Metallo-dependent phosphatases
(115)
Superfamily
:
Metallo-dependent phosphatases
(115)
Family
:
Purple acid phosphatase-like
(14)
Protein domain
:
automated matches
(7)
French bean (Phaseolus vulgaris) [TaxId: 3885]
(5)
2a
d2qfpa2
A:121-432
2b
d2qfpb2
B:121-432
2c
d2qfpc2
C:121-432
2d
d2qfpd2
D:121-432
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_2qfpA02 (A:123-432)
1b: CATH_2qfpB02 (B:123-432)
1c: CATH_2qfpC02 (C:123-432)
1d: CATH_2qfpD02 (D:123-432)
2a: CATH_2qfpA01 (A:26-122)
2b: CATH_2qfpB01 (B:26-122)
2c: CATH_2qfpC01 (C:26-122)
2d: CATH_2qfpD01 (D:26-122)
View:
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(
)
(
)
Architectures
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)
(
)
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)
Kidney bean (Phaseolus vulgaris)
(2)
1a
2qfpA02
A:123-432
1b
2qfpB02
B:123-432
1c
2qfpC02
C:123-432
1d
2qfpD02
D:123-432
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Purple acid phosphatase, domain1
(6)
Kidney bean (Phaseolus vulgaris)
(2)
2a
2qfpA01
A:26-122
2b
2qfpB01
B:26-122
2c
2qfpC01
C:26-122
2d
2qfpD01
D:26-122
[
close CATH info
]
Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_Metallophos_2qfpD01 (D:101-300)
1b: PFAM_Metallophos_2qfpD02 (D:101-300)
1c: PFAM_Metallophos_2qfpD03 (D:101-300)
1d: PFAM_Metallophos_2qfpD04 (D:101-300)
2a: PFAM_Metallophos_C_2qfpD05 (D:325-391)
2b: PFAM_Metallophos_C_2qfpD06 (D:325-391)
2c: PFAM_Metallophos_C_2qfpD07 (D:325-391)
2d: PFAM_Metallophos_C_2qfpD08 (D:325-391)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Calcineurin
(56)
Family
:
Metallophos
(45)
Phaseolus vulgaris (Kidney bean) (French bean)
(4)
1a
Metallophos-2qfpD01
D:101-300
1b
Metallophos-2qfpD02
D:101-300
1c
Metallophos-2qfpD03
D:101-300
1d
Metallophos-2qfpD04
D:101-300
Clan
:
no clan defined [family: Metallophos_C]
(5)
Family
:
Metallophos_C
(5)
Phaseolus vulgaris (Kidney bean) (French bean)
(4)
2a
Metallophos_C-2qfpD05
D:325-391
2b
Metallophos_C-2qfpD06
D:325-391
2c
Metallophos_C-2qfpD07
D:325-391
2d
Metallophos_C-2qfpD08
D:325-391
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