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2QFP
Asym. Unit
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
[
close entry info
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Hetero Components
(7, 47)
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
4
Ligand/Ion
FLUORIDE ION
2
FE
4
Ligand/Ion
FE (III) ION
3
NA
11
Ligand/Ion
SODIUM ION
4
NAG
13
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
5
NDG
3
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
6
SO4
8
Ligand/Ion
SULFATE ION
7
ZN
4
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(47, 47)
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)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
45: EC9 (SOFTWARE)
46: FC1 (SOFTWARE)
47: 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
AC2
SOFTWARE
ASP A:16 , VAL A:17 , ASN A:143 , SER A:147
BINDING SITE FOR RESIDUE NAG A 438
03
AC3
SOFTWARE
LYS A:395 , ASN A:396 , THR A:398 , TRP A:419
BINDING SITE FOR RESIDUE NAG A 439
04
AC4
SOFTWARE
ARG A:108 , ASN A:109
BINDING SITE FOR RESIDUE NAG A 440
05
AC5
SOFTWARE
ASN B:81 , ASN B:173 , TYR C:24
BINDING SITE FOR RESIDUE NAG B 437
06
AC6
SOFTWARE
ASP B:16 , PHE B:140 , ASN B:143 , SER B:147 , ARG B:188
BINDING SITE FOR RESIDUE NDG B 438
07
AC7
SOFTWARE
ASN B:396 , THR B:398 , HIS B:399
BINDING SITE FOR RESIDUE NDG B 439
08
AC8
SOFTWARE
GLU B:51 , ARG B:108 , ASN B:109
BINDING SITE FOR RESIDUE NAG B 440
09
AC9
SOFTWARE
TYR B:24 , ASP B:50 , ASN C:81
BINDING SITE FOR RESIDUE NAG C 437
10
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
11
BC2
SOFTWARE
ASN C:396 , HIS C:399 , TRP C:419
BINDING SITE FOR RESIDUE NDG C 439
12
BC3
SOFTWARE
GLU C:51 , ARG C:108 , ASN C:109
BINDING SITE FOR RESIDUE NAG C 440
13
BC4
SOFTWARE
TYR A:24 , ASN D:81 , ASN D:173
BINDING SITE FOR RESIDUE NAG D 437
14
BC5
SOFTWARE
ASP D:16 , PHE D:140 , ASN D:143 , SER D:147
BINDING SITE FOR RESIDUE NAG D 438
15
BC6
SOFTWARE
LYS D:395 , ASN D:396
BINDING SITE FOR RESIDUE NAG D 439
16
BC7
SOFTWARE
ARG D:108 , ASN D:109
BINDING SITE FOR RESIDUE NAG D 440
17
BC8
SOFTWARE
ASP A:135 , ASP A:164 , TYR A:167 , HIS A:325 , ZN A:434 , F A:436
BINDING SITE FOR RESIDUE FE A 433
18
BC9
SOFTWARE
ASP A:135 , ASP A:164 , ASN A:201 , HIS A:286 , HIS A:323 , FE A:433 , F A:436
BINDING SITE FOR RESIDUE ZN A 434
19
CC1
SOFTWARE
HIS A:202 , HIS A:325 , TYR A:365 , F A:436 , NA A:442 , NA A:444 , HOH A:594 , SO4 B:441
BINDING SITE FOR RESIDUE SO4 A 435
20
CC2
SOFTWARE
ASP A:164 , ASN A:201 , HIS A:323 , FE A:433 , ZN A:434 , SO4 A:435 , NA A:442 , HOH A:594
BINDING SITE FOR RESIDUE F A 436
21
CC3
SOFTWARE
HIS A:296 , SO4 A:435 , NA A:442 , NA A:443 , NA A:444 , ARG B:258 , HOH B:473
BINDING SITE FOR RESIDUE SO4 B 441
22
CC4
SOFTWARE
ASN A:201 , HIS A:202 , HIS A:296 , SO4 A:435 , F A:436 , HOH A:594 , SO4 B:441
BINDING SITE FOR RESIDUE NA A 442
23
CC5
SOFTWARE
HIS A:295 , NA A:444 , ARG B:258 , SO4 B:441
BINDING SITE FOR RESIDUE NA A 443
24
CC6
SOFTWARE
HIS A:295 , SO4 A:435 , NA A:443 , SO4 B:441
BINDING SITE FOR RESIDUE NA A 444
25
CC7
SOFTWARE
ASP B:135 , ASP B:164 , TYR B:167 , HIS B:325 , ZN B:434 , F B:436
BINDING SITE FOR RESIDUE FE B 433
26
CC8
SOFTWARE
ASP B:135 , ASP B:164 , ASN B:201 , HIS B:286 , HIS B:323 , FE B:433 , F B:436
BINDING SITE FOR RESIDUE ZN B 434
27
CC9
SOFTWARE
SO4 A:441 , HIS B:202 , HIS B:325 , TYR B:365 , F B:436 , NA B:442 , NA B:444
BINDING SITE FOR RESIDUE SO4 B 435
28
DC1
SOFTWARE
ASP B:135 , ASP B:164 , ASN B:201 , HIS B:323 , HIS B:325 , FE B:433 , ZN B:434 , SO4 B:435 , NA B:442
BINDING SITE FOR RESIDUE F B 436
29
DC2
SOFTWARE
ARG A:258 , HIS B:296 , SO4 B:435 , NA B:442 , NA B:443 , NA B:444
BINDING SITE FOR RESIDUE SO4 A 441
30
DC3
SOFTWARE
SO4 A:441 , ASN B:201 , HIS B:296 , SO4 B:435 , F B:436
BINDING SITE FOR RESIDUE NA B 442
31
DC4
SOFTWARE
SO4 A:441 , HIS B:295 , NA B:444
BINDING SITE FOR RESIDUE NA B 443
32
DC5
SOFTWARE
SO4 A:441 , HIS B:295 , SO4 B:435 , NA B:443
BINDING SITE FOR RESIDUE NA B 444
33
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
34
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
35
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
36
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
37
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
38
EC2
SOFTWARE
HIS C:295 , NA C:444 , SO4 D:441
BINDING SITE FOR RESIDUE NA C 442
39
EC3
SOFTWARE
ASN C:201 , HIS C:296 , SO4 C:435 , F C:436
BINDING SITE FOR RESIDUE NA C 443
40
EC4
SOFTWARE
HIS C:295 , SO4 C:435 , NA C:442 , SO4 D:441
BINDING SITE FOR RESIDUE NA C 444
41
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
42
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
43
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
44
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
45
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
46
FC1
SOFTWARE
SO4 C:441 , HIS D:295
BINDING SITE FOR RESIDUE NA D 442
47
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 not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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_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)
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Clans
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Families
(
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(
)
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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