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4DUR
Asym. Unit
Info
Asym.Unit (548 KB)
Biol.Unit 1 (275 KB)
Biol.Unit 2 (270 KB)
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(1)
Title
:
THE X-RAY CRYSTAL STRUCTURE OF FULL-LENGTH TYPE II HUMAN PLASMINOGEN
Authors
:
R. H. P. Law, T. Caradoc-Davies, J. C. Whisstock
Date
:
22 Feb 12 (Deposition) - 28 Mar 12 (Release) - 26 Jun 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.45
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Serine Protease, Fibrinolysis, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. H. P. Law, T. Caradoc-Davies, N. Cowieson, A. J. Horvath, A. J. Quek, J. A. Encarnacao, D. Steer, A. Cowan, Q. Zhang, B. G. C. Lu, R. N. Pike, A. I. Smith, P. B. Coughlin, J. C. Whisstock
The X-Ray Crystal Structure Of Full-Length Human Plasminoge
Cell Rep V. 1 185 2012
[
close entry info
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Hetero Components
(7, 18)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
2a: BICARBONATE ION (BCTa)
2b: BICARBONATE ION (BCTb)
3a: CHLORIDE ION (CLa)
3b: CHLORIDE ION (CLb)
3c: CHLORIDE ION (CLc)
3d: CHLORIDE ION (CLd)
3e: CHLORIDE ION (CLe)
3f: CHLORIDE ION (CLf)
3g: CHLORIDE ION (CLg)
4a: BETA-D-GALACTOSE (GALa)
4b: BETA-D-GALACTOSE (GALb)
5a: POTASSIUM ION (Ka)
5b: POTASSIUM ION (Kb)
6a: N-ACETYL-D-GLUCOSAMINE (NAGa)
6b: N-ACETYL-D-GLUCOSAMINE (NAGb)
7a: O-SIALIC ACID (SIAa)
7b: O-SIALIC ACID (SIAb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
1
Ligand/Ion
ACETATE ION
2
BCT
2
Ligand/Ion
BICARBONATE ION
3
CL
7
Ligand/Ion
CHLORIDE ION
4
GAL
2
Ligand/Ion
BETA-D-GALACTOSE
5
K
2
Ligand/Ion
POTASSIUM ION
6
NAG
2
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
7
SIA
2
Ligand/Ion
O-SIALIC ACID
[
close Hetero Component info
]
Sites
(18, 18)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:68 , LYS A:392 , PHE A:419 , ARG A:426 , HOH A:954
BINDING SITE FOR RESIDUE CL A 801
02
AC2
SOFTWARE
PHE A:205 , ASN A:207 , HOH A:1270
BINDING SITE FOR RESIDUE CL A 802
03
AC3
SOFTWARE
ARG A:234 , LYS A:708 , ASN A:711 , HOH A:1290
BINDING SITE FOR RESIDUE CL A 803
04
AC4
SOFTWARE
HIS A:621 , GLN A:622 , GLU A:627 , HOH A:1588
BINDING SITE FOR RESIDUE CL A 804
05
AC5
SOFTWARE
SER A:170 , ARG A:220 , GLU A:221 , ASN A:294 , HOH A:1063 , HOH A:1374 , HOH A:1375
BINDING SITE FOR RESIDUE K A 805
06
AC6
SOFTWARE
ILE A:682 , GLY A:684 , GLY A:739
BINDING SITE FOR RESIDUE BCT A 806
07
AC7
SOFTWARE
ARG A:117 , TRP A:144 , TYR A:146 , ARG A:153 , HOH A:1508 , HOH B:1401 , HOH B:1531
BINDING SITE FOR RESIDUE ACT A 807
08
AC8
SOFTWARE
THR A:346 , PRO A:348 , PRO A:349 , GAL A:809 , HOH A:1627
BINDING SITE FOR RESIDUE NAG A 808
09
AC9
SOFTWARE
NAG A:808 , SIA A:810
BINDING SITE FOR RESIDUE GAL A 809
10
BC1
SOFTWARE
GAL A:809 , HOH A:1501
BINDING SITE FOR RESIDUE SIA A 810
11
BC2
SOFTWARE
ARG B:68 , LYS B:392 , PHE B:419 , ARG B:426 , HOH B:1283
BINDING SITE FOR RESIDUE CL B 801
12
BC3
SOFTWARE
ARG B:234 , ASN B:711 , HOH B:1520
BINDING SITE FOR RESIDUE CL B 802
13
BC4
SOFTWARE
PHE B:205 , ASN B:207 , HOH B:1321 , HOH B:1338
BINDING SITE FOR RESIDUE CL B 803
14
BC5
SOFTWARE
SER B:170 , ARG B:220 , GLU B:221 , ASN B:294 , HOH B:1214 , HOH B:1292 , HOH B:1574
BINDING SITE FOR RESIDUE K B 804
15
BC6
SOFTWARE
ILE B:682 , LYS B:698 , GLY B:739
BINDING SITE FOR RESIDUE BCT B 805
16
BC7
SOFTWARE
THR B:346 , PRO B:348 , GAL B:807
BINDING SITE FOR RESIDUE NAG B 806
17
BC8
SOFTWARE
NAG B:806 , SIA B:808
BINDING SITE FOR RESIDUE GAL B 807
18
BC9
SOFTWARE
GAL B:807
BINDING SITE FOR RESIDUE SIA B 808
[
close Site info
]
SAPs(SNPs)/Variants
(18, 34)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_018657 (K19E, chain A/B, )
02: VAR_011779 (I27R, chain A/B, )
03: VAR_016287 (E38K, chain A/B, )
04: VAR_016288 (H114Q, chain A/B, )
05: VAR_033653 (R115K, chain A/B, )
06: VAR_018658 (L128P, chain A/B, )
07: VAR_018659 (R216H, chain A/B, )
08: VAR_016289 (R242H, chain A/B, )
09: VAR_006627 (V355F, chain A/B, )
10: VAR_016290 (R389W, chain A/B, )
11: VAR_011780 (K434I, chain A/B, )
12: VAR_016292 (A475V, chain A, )
13: VAR_016293 (R504W, chain A, )
14: VAR_018660 (R513H, chain A/B, )
15: VAR_006628 (S572P, chain A/B, )
16: VAR_006629 (A601T, chain A/B, )
17: VAR_031213 (V657D, chain A/B, )
18: VAR_006630 (G732R, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_018657
K
38
E
PLMN_HUMAN
Disease (PLGD)
73015965
A/B
K
19
E
02
UniProt
VAR_011779
I
46
R
PLMN_HUMAN
Polymorphism
1049573
A/B
I
27
R
03
UniProt
VAR_016287
E
57
K
PLMN_HUMAN
Polymorphism
4252070
A/B
E
38
K
04
UniProt
VAR_016288
H
133
Q
PLMN_HUMAN
Polymorphism
4252186
A/B
H
114
Q
05
UniProt
VAR_033653
R
134
K
PLMN_HUMAN
Polymorphism
2817
A/B
R
115
K
06
UniProt
VAR_018658
L
147
P
PLMN_HUMAN
Disease (PLGD)
---
A/B
L
128
P
07
UniProt
VAR_018659
R
235
H
PLMN_HUMAN
Disease (PLGD)
---
A/B
R
216
H
08
UniProt
VAR_016289
R
261
H
PLMN_HUMAN
Polymorphism
4252187
A/B
R
242
H
09
UniProt
VAR_006627
V
374
F
PLMN_HUMAN
Disease (PLGD)
121918028
A/B
V
355
F
10
UniProt
VAR_016290
R
408
W
PLMN_HUMAN
Polymorphism
4252119
A/B
R
389
W
11
UniProt
VAR_011780
K
453
I
PLMN_HUMAN
Polymorphism
1804181
A/B
K
434
I
12
UniProt
VAR_016292
A
494
V
PLMN_HUMAN
Polymorphism
4252128
A
A
475
V
13
UniProt
VAR_016293
R
523
W
PLMN_HUMAN
Polymorphism
4252129
A
R
504
W
14
UniProt
VAR_018660
R
532
H
PLMN_HUMAN
Disease (PLGD)
---
A/B
R
513
H
15
UniProt
VAR_006628
S
591
P
PLMN_HUMAN
Disease (PLGD)
---
A/B
S
572
P
16
UniProt
VAR_006629
A
620
T
PLMN_HUMAN
Disease (PLGD)
121918027
A/B
A
601
T
17
UniProt
VAR_031213
V
676
D
PLMN_HUMAN
Polymorphism
17857492
A/B
V
657
D
18
UniProt
VAR_006630
G
751
R
PLMN_HUMAN
Disease (PLGD)
---
A/B
G
732
R
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(5, 26)
Info
All PROSITE Patterns/Profiles
1: KRINGLE_2 (A:83-162,B:83-162|A:165-243,B:165-...)
2: KRINGLE_1 (A:132-145,B:132-145|A:214-226,B:21...)
3: TRYPSIN_DOM (A:562-789,B:562-789)
4: TRYPSIN_HIS (A:599-604,B:599-604)
5: TRYPSIN_SER (A:735-746,B:735-746)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
KRINGLE_2
PS50070
Kringle domain profile.
PLMN_HUMAN
102-181
184-262
274-352
376-454
480-560
10
A:83-162
B:83-162
A:165-243
B:165-243
A:255-333
B:255-333
A:357-435
B:357-435
A:461-541
B:461-541
2
KRINGLE_1
PS00021
Kringle domain signature.
PLMN_HUMAN
151-164
233-245
323-335
425-437
530-543
10
A:132-145
B:132-145
A:214-226
B:214-226
A:304-316
B:304-316
A:406-418
B:406-418
A:511-524
B:511-524
3
TRYPSIN_DOM
PS50240
Serine proteases, trypsin domain profile.
PLMN_HUMAN
581-808
2
A:562-789
B:562-789
4
TRYPSIN_HIS
PS00134
Serine proteases, trypsin family, histidine active site.
PLMN_HUMAN
618-623
2
A:599-604
B:599-604
5
TRYPSIN_SER
PS00135
Serine proteases, trypsin family, serine active site.
PLMN_HUMAN
754-765
2
A:735-746
B:735-746
[
close PROSITE info
]
Exons
(18, 36)
Info
All Exons
Exon 1.2d (A:3-43 | B:2-43)
Exon 1.3a (A:43-79 | B:43-79)
Exon 1.4a (A:79-117 | B:79-117)
Exon 1.5b (A:117-164 | B:117-164)
Exon 1.6 (A:164-204 | B:164-204)
Exon 1.7 (A:204-244 | B:204-244)
Exon 1.8 (A:244-298 | B:244-298)
Exon 1.9 (A:298-347 (gaps) | B:298-347 (gaps...)
Exon 1.10 (A:347-400 | B:347-400)
Exon 1.11c (A:400-461 (gaps) | B:400-461 (gaps...)
Exon 1.12b (A:461-510 | B:461-510 (gaps))
Exon 1.13 (A:511-542 | B:511-541)
Exon 1.14 (A:542-582 | B:544-582)
Exon 1.15b (A:582-607 | B:582-607)
Exon 1.16 (A:607-654 | B:607-654)
Exon 1.17b (A:654-688 | B:654-687)
Exon 1.18b (A:692-738 | B:691-738)
Exon 1.19b (A:739-791 | B:739-791)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.1b/1.2d
02: Boundary 1.2d/1.3a
03: Boundary 1.3a/1.4a
04: Boundary 1.4a/1.5b
05: Boundary 1.5b/1.6
06: Boundary 1.6/1.7
07: Boundary 1.7/1.8
08: Boundary 1.8/1.9
09: Boundary 1.9/1.10
10: Boundary 1.10/1.11c
11: Boundary 1.11c/1.12b
12: Boundary 1.12b/1.13
13: Boundary 1.13/1.14
14: Boundary 1.14/1.15b
15: Boundary 1.15b/1.16
16: Boundary 1.16/1.17b
17: Boundary 1.17b/1.18b
18: Boundary 1.18b/1.19b
19: Boundary 1.19b/-
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
1.1b
ENST00000308192
1b
ENSE00001900502
chr6:
161123274-161123385
112
PLMN_HUMAN
1-17
17
0
-
-
1.2d
ENST00000308192
2d
ENSE00002186994
chr6:
161127439-161127574
136
PLMN_HUMAN
17-62
46
2
A:3-43
B:2-43
41
42
1.3a
ENST00000308192
3a
ENSE00002162767
chr6:
161128732-161128838
107
PLMN_HUMAN
62-98
37
2
A:43-79
B:43-79
37
37
1.4a
ENST00000308192
4a
ENSE00002147931
chr6:
161132109-161132223
115
PLMN_HUMAN
98-136
39
2
A:79-117
B:79-117
39
39
1.5b
ENST00000308192
5b
ENSE00002160428
chr6:
161134018-161134157
140
PLMN_HUMAN
136-183
48
2
A:117-164
B:117-164
48
48
1.6
ENST00000308192
6
ENSE00002153394
chr6:
161135826-161135946
121
PLMN_HUMAN
183-223
41
2
A:164-204
B:164-204
41
41
1.7
ENST00000308192
7
ENSE00002185478
chr6:
161137677-161137795
119
PLMN_HUMAN
223-263
41
2
A:204-244
B:204-244
41
41
1.8
ENST00000308192
8
ENSE00002162125
chr6:
161139326-161139488
163
PLMN_HUMAN
263-317
55
2
A:244-298
B:244-298
55
55
1.9
ENST00000308192
9
ENSE00002174772
chr6:
161139725-161139870
146
PLMN_HUMAN
317-366
50
2
A:298-347 (gaps)
B:298-347 (gaps)
50
50
1.10
ENST00000308192
10
ENSE00002171287
chr6:
161143440-161143599
160
PLMN_HUMAN
366-419
54
2
A:347-400
B:347-400
54
54
1.11c
ENST00000308192
11c
ENSE00002163078
chr6:
161152083-161152264
182
PLMN_HUMAN
419-480
62
2
A:400-461 (gaps)
B:400-461 (gaps)
62
62
1.12b
ENST00000308192
12b
ENSE00002160674
chr6:
161152777-161152925
149
PLMN_HUMAN
480-529
50
2
A:461-510
B:461-510 (gaps)
50
50
1.13
ENST00000308192
13
ENSE00002175196
chr6:
161155027-161155120
94
PLMN_HUMAN
530-561
32
2
A:511-542
B:511-541
32
31
1.14
ENST00000308192
14
ENSE00002152595
chr6:
161157919-161158039
121
PLMN_HUMAN
561-601
41
2
A:542-582
B:544-582
41
39
1.15b
ENST00000308192
15b
ENSE00002177616
chr6:
161159570-161159644
75
PLMN_HUMAN
601-626
26
2
A:582-607
B:582-607
26
26
1.16
ENST00000308192
16
ENSE00002172545
chr6:
161160100-161160240
141
PLMN_HUMAN
626-673
48
2
A:607-654
B:607-654
48
48
1.17b
ENST00000308192
17b
ENSE00002178747
chr6:
161162343-161162449
107
PLMN_HUMAN
673-709
37
2
A:654-688
B:654-687
35
34
1.18b
ENST00000308192
18b
ENSE00002181703
chr6:
161173147-161173292
146
PLMN_HUMAN
709-757
49
2
A:692-738
B:691-738
47
48
1.19b
ENST00000308192
19b
ENSE00001864790
chr6:
161173932-161174338
407
PLMN_HUMAN
758-810
53
2
A:739-791
B:739-791
53
53
[
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SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
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CATH Domains
(0, 0)
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all CATH domains
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Asym.Unit (548 KB)
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