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Asym. Unit
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Asym.Unit (165 KB)
Biol.Unit 1 (158 KB)
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(1)
Title
:
CRYSTAL STRCTURE OF HUMAN PROLIDASE
Authors
:
U. Mueller, F. H. Niesen, Y. Roske, F. Goetz, J. Behlke, K. Buessow, U. He Protein Structure Factory (Psf)
Date
:
17 Jan 07 (Deposition) - 20 Feb 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.45
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Metallocarboxypeptidase, Disease Mutation, Xaa-Pro Dipeptidase, Dipeptidase, Peptidase D, Collagen Degradation, Metalloaminopeptidase, Enzyme, Protease, Pepd Gene, Manganese, Hydrolase, Metal-Binding, Metalloprotease, Phosphorylation, Structural Genomics, Protein Structure Factory, Psf
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
U. Mueller, F. H. Niesen, Y. Roske, F. Goetz, J. Behlke, K. Buessow, U. Heinemann
Crystal Structure Of Human Prolidase: The Molecular Basis O Pd Disease.
To Be Published
[
close entry info
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Hetero Components
(2, 7)
Info
All Hetero Components
1a: MANGANESE (II) ION (MNa)
1b: MANGANESE (II) ION (MNb)
1c: MANGANESE (II) ION (MNc)
1d: MANGANESE (II) ION (MNd)
2a: HYDROGENPHOSPHATE ION (PIa)
2b: HYDROGENPHOSPHATE ION (PIb)
2c: HYDROGENPHOSPHATE ION (PIc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MN
4
Ligand/Ion
MANGANESE (II) ION
2
PI
3
Ligand/Ion
HYDROGENPHOSPHATE ION
[
close Hetero Component info
]
Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:288 , HIS A:371 , GLU A:413 , GLU A:453 , MN A:496 , PI A:501
BINDING SITE FOR RESIDUE MN A 495
2
AC2
SOFTWARE
ASP A:277 , ASP A:288 , GLU A:453 , MN A:495 , PI A:501
BINDING SITE FOR RESIDUE MN A 496
3
AC3
SOFTWARE
ASP B:288 , HIS B:371 , GLU B:413 , GLU B:453 , MN B:496 , PI B:502
BINDING SITE FOR RESIDUE MN B 495
4
AC4
SOFTWARE
ASP B:277 , ASP B:288 , GLU B:453 , MN B:495 , PI B:502 , HOH B:567
BINDING SITE FOR RESIDUE MN B 496
5
AC5
SOFTWARE
ASP A:277 , ASP A:288 , HIS A:371 , HIS A:378 , GLU A:413 , GLU A:453 , MN A:495 , MN A:496 , HOH A:503
BINDING SITE FOR RESIDUE PI A 501
6
AC6
SOFTWARE
HIS B:256 , ASP B:277 , ASP B:288 , HIS B:371 , HIS B:378 , GLU B:413 , GLU B:453 , MN B:495 , MN B:496 , HOH B:567 , HOH B:573
BINDING SITE FOR RESIDUE PI B 502
7
AC7
SOFTWARE
VAL B:387 , HIS B:403 , GLN B:405 , HOH B:563
BINDING SITE FOR RESIDUE PI B 503
[
close Site info
]
SAPs(SNPs)/Variants
(6, 12)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_011614 (R185Q, chain A/B, )
2: VAR_004404 (D277N, chain A/B, )
3: VAR_011615 (G279D, chain A/B, )
4: VAR_051574 (R389H, chain A/B, )
5: VAR_014723 (F436F, chain A/B, )
6: VAR_004405 (G449R, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_011614
R
184
Q
PEPD_HUMAN
Disease (PD)
---
A/B
R
185
Q
2
UniProt
VAR_004404
D
276
N
PEPD_HUMAN
Disease (PD)
---
A/B
D
277
N
3
UniProt
VAR_011615
G
278
D
PEPD_HUMAN
Disease (PD)
---
A/B
G
279
D
4
UniProt
VAR_051574
R
388
H
PEPD_HUMAN
Polymorphism
2230062
A/B
R
389
H
5
UniProt
VAR_014723
L
435
F
PEPD_HUMAN
Polymorphism
17570
A/B
F
436
F
6
UniProt
VAR_004405
G
448
R
PEPD_HUMAN
Disease (PD)
---
A/B
G
449
R
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: PROLINE_PEPTIDASE (A:367-379,B:367-379)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PROLINE_PEPTIDASE
PS00491
Aminopeptidase P and proline dipeptidase signature.
PEPD_HUMAN
366-378
2
A:367-379
B:367-379
[
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Exons
(15, 30)
Info
All Exons
Exon 1.1 (A:7-7 | B:7-7)
Exon 1.2 (A:7-68 | B:7-68)
Exon 1.3 (A:69-111 | B:69-111)
Exon 1.4 (A:111-132 | B:111-132)
Exon 1.5 (A:133-148 | B:133-148)
Exon 1.6 (A:149-169 | B:149-169)
Exon 1.7 (A:169-184 | B:169-184)
Exon 1.8 (A:184-209 | B:184-209)
Exon 1.9 (A:210-225 | B:210-225)
Exon 1.10 (A:225-248 | B:225-248)
Exon 1.11 (A:248-274 | B:248-274)
Exon 1.12 (A:274-324 | B:274-324)
Exon 1.13 (A:324-385 | B:324-385)
Exon 1.14 (A:386-449 | B:386-449)
Exon 1.15 (A:450-483 | B:450-483)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1
02: Boundary 1.1/1.2
03: Boundary 1.2/1.3
04: Boundary 1.3/1.4
05: Boundary 1.4/1.5
06: Boundary 1.5/1.6
07: Boundary 1.6/1.7
08: Boundary 1.7/1.8
09: Boundary 1.8/1.9
10: Boundary 1.9/1.10
11: Boundary 1.10/1.11
12: Boundary 1.11/1.12
13: Boundary 1.12/1.13
14: Boundary 1.13/1.14
15: Boundary 1.14/1.15
16: Boundary 1.15/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
ENST00000244137
1
ENSE00001356571
chr19:
34012801-34012650
152
PEPD_HUMAN
1-6
6
2
A:7-7
B:7-7
1
1
1.2
ENST00000244137
2
ENSE00000896667
chr19:
34003682-34003499
184
PEPD_HUMAN
6-67
62
2
A:7-68
B:7-68
62
62
1.3
ENST00000244137
3
ENSE00000896666
chr19:
34002061-34001934
128
PEPD_HUMAN
68-110
43
2
A:69-111
B:69-111
43
43
1.4
ENST00000244137
4
ENSE00000953262
chr19:
33991907-33991844
64
PEPD_HUMAN
110-131
22
2
A:111-132
B:111-132
22
22
1.5
ENST00000244137
5
ENSE00001012845
chr19:
33984243-33984196
48
PEPD_HUMAN
132-147
16
2
A:133-148
B:133-148
16
16
1.6
ENST00000244137
6
ENSE00000953263
chr19:
33980963-33980902
62
PEPD_HUMAN
148-168
21
2
A:149-169
B:149-169
21
21
1.7
ENST00000244137
7
ENSE00000896664
chr19:
33968996-33968952
45
PEPD_HUMAN
168-183
16
2
A:169-184
B:169-184
16
16
1.8
ENST00000244137
8
ENSE00000695478
chr19:
33954968-33954893
76
PEPD_HUMAN
183-208
26
2
A:184-209
B:184-209
26
26
1.9
ENST00000244137
9
ENSE00000695480
chr19:
33953947-33953901
47
PEPD_HUMAN
209-224
16
2
A:210-225
B:210-225
16
16
1.10
ENST00000244137
10
ENSE00000896661
chr19:
33904549-33904481
69
PEPD_HUMAN
224-247
24
2
A:225-248
B:225-248
24
24
1.11
ENST00000244137
11
ENSE00000896659
chr19:
33902655-33902578
78
PEPD_HUMAN
247-273
27
2
A:248-274
B:248-274
27
27
1.12
ENST00000244137
12
ENSE00000896656
chr19:
33892775-33892627
149
PEPD_HUMAN
273-323
51
2
A:274-324
B:274-324
51
51
1.13
ENST00000244137
13
ENSE00000695490
chr19:
33882385-33882201
185
PEPD_HUMAN
323-384
62
2
A:324-385
B:324-385
62
62
1.14
ENST00000244137
14
ENSE00001261724
chr19:
33878987-33878796
192
PEPD_HUMAN
385-448
64
2
A:386-449
B:386-449
64
64
1.15
ENST00000244137
15
ENSE00000846271
chr19:
33878387-33877865
523
PEPD_HUMAN
449-493
45
2
A:450-483
B:450-483
34
34
[
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]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_AMP_N_2oknB01 (B:19-156)
1b: PFAM_AMP_N_2oknB02 (B:19-156)
2a: PFAM_Peptidase_M24_2oknB03 (B:194-460)
2b: PFAM_Peptidase_M24_2oknB04 (B:194-460)
View:
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Clans
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)
(
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Families
(
)
(
)
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(
)
(
)
Clan
:
AMP_N-like
(22)
Family
:
AMP_N
(11)
Homo sapiens (Human)
(1)
1a
AMP_N-2oknB01
B:19-156
1b
AMP_N-2oknB02
B:19-156
Clan
:
no clan defined [family: Peptidase_M24]
(23)
Family
:
Peptidase_M24
(23)
Homo sapiens (Human)
(2)
2a
Peptidase_M24-2oknB03
B:194-460
2b
Peptidase_M24-2oknB04
B:194-460
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