PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
3BT1
Asym. Unit
Info
Asym.Unit (78 KB)
Biol.Unit 1 (71 KB)
Biol.Unit 2 (65 KB)
Biol.Unit 3 (9 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF UROKINASE RECEPTOR, UROKINASE AND VITRONECTIN COMPLEX
Authors
:
M. Huang
Date
:
27 Dec 07 (Deposition) - 25 Mar 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,U
Biol. Unit 1: A,B,U (1x)
Biol. Unit 2: A,U (1x)
Biol. Unit 3: B (1x)
Keywords
:
Protein-Protein Complex, Glycoprotein, Gpi-Anchor, Lipoprotein, Membrane, Receptor, Secreted, Blood Coagulation, Egf-Like Domain, Fibrinolysis, Hydrolase, Kringle, Phosphoprotein, Plasminogen Activation, Protease, Serine Protease, Zymogen, Cell Adhesion, Heparin-Binding, Sulfation, Immunoglobulin Domain, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Q. Huai, A. Zhou, L. Lin, A. P. Mazar, G. C. Parry, J. Callahan, D. E. Shaw B. Furie, B. C. Furie, M. Huang
Crystal Structures Of Two Human Vitronectin, Urokinase And Urokinase Receptor Complexes
Nat. Struct. Mol. Biol. V. 15 422 2008
[
close entry info
]
Hetero Components
(2, 5)
Info
All Hetero Components
1a: ALPHA-D-MANNOSE (MANa)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2b: N-ACETYL-D-GLUCOSAMINE (NAGb)
2c: N-ACETYL-D-GLUCOSAMINE (NAGc)
2d: N-ACETYL-D-GLUCOSAMINE (NAGd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MAN
1
Ligand/Ion
ALPHA-D-MANNOSE
2
NAG
4
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN U:52
BINDING SITE FOR RESIDUE NAG U 1052
2
AC2
SOFTWARE
MET A:67 , MET A:127 , ASN U:172
BINDING SITE FOR RESIDUE NAG U 1172
3
AC3
SOFTWARE
ASN U:200 , THR U:202 , HIS U:203
BINDING SITE FOR RESIDUE NAG U 1200
4
AC4
SOFTWARE
HIS U:203
BINDING SITE FOR RESIDUE NAG U 1201
5
AC5
SOFTWARE
GLU B:23
BINDING SITE FOR RESIDUE MAN U 1202
[
close Site info
]
SAPs(SNPs)/Variants
(6, 6)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_016322 (E33G, chain U, )
2: VAR_016323 (T64A, chain U, )
3: VAR_006722 (P121L, chain A, )
4: VAR_016325 (K198R, chain U, )
5: VAR_016326 (N259K, chain U, )
6: VAR_052698 (D275A, chain U, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_016322
E
55
G
UPAR_HUMAN
Polymorphism
4251813
U
E
33
G
2
UniProt
VAR_016323
T
86
A
UPAR_HUMAN
Polymorphism
399145
U
T
64
A
3
UniProt
VAR_006722
P
141
L
UROK_HUMAN
Polymorphism
2227564
A
P
121
L
4
UniProt
VAR_016325
K
220
R
UPAR_HUMAN
Polymorphism
2302524
U
K
198
R
5
UniProt
VAR_016326
N
281
K
UPAR_HUMAN
Polymorphism
4251921
U
N
259
K
6
UniProt
VAR_052698
D
297
A
UPAR_HUMAN
Polymorphism
16976608
U
D
275
A
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(5, 7)
Info
All PROSITE Patterns/Profiles
1: LY6_UPAR (U:2-45|U:94-147|U:193-247)
2: SMB_1 (B:19-39)
3: EGF_1 (A:31-42)
4: KRINGLE_2 (A:49-131)
5: KRINGLE_1 (A:101-113)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
LY6_UPAR
PS00983
Ly-6 / u-PAR domain signature.
UPAR_HUMAN
24-67
116-169
215-269
3
U:2-45
U:94-147
U:193-247
2
SMB_1
PS00524
Somatomedin B domain (SMB) signature.
VTNC_HUMAN
38-58
1
B:19-39
3
EGF_1
PS00022
EGF-like domain signature 1.
UROK_HUMAN
51-62
1
A:31-42
4
KRINGLE_2
PS50070
Kringle domain profile.
UROK_HUMAN
69-151
1
A:49-131
5
KRINGLE_1
PS00021
Kringle domain signature.
UROK_HUMAN
121-133
1
A:101-113
[
close PROSITE info
]
Exons
(12, 12)
Info
All Exons
Exon 1.1 (B:2-3)
Exon 1.2 (B:3-41)
Exon 2.2 (U:1-34)
Exon 2.3 (U:34-82)
Exon 2.4 (U:82-136 (gaps))
Exon 2.5 (U:136-181)
Exon 2.6 (U:181-230)
Exon 2.7 (U:230-275)
Exon 3.5 (A:8-9)
Exon 3.6a (A:9-45)
Exon 3.7b (A:45-103)
Exon 3.8 (A:103-132)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1
02: Boundary 1.1/1.2
03: Boundary 1.2/1.3
04: Boundary 2.1/2.2
05: Boundary 2.2/2.3
06: Boundary 2.3/2.4
07: Boundary 2.4/2.5
08: Boundary 2.5/2.6
09: Boundary 2.6/2.7
10: Boundary 2.7/-
11: Boundary 3.4b/3.5
12: Boundary 3.5/3.6a
13: Boundary 3.6a/3.7b
14: Boundary 3.7b/3.8
15: Boundary 3.8/3.9b
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
ENST00000226218
1
ENSE00001177296
chr17:
26697717-26697161
557
VTNC_HUMAN
1-22
22
1
B:2-3
2
1.2
ENST00000226218
2
ENSE00000705689
chr17:
26697067-26696948
120
VTNC_HUMAN
22-62
41
1
B:3-41
39
1.3
ENST00000226218
3
ENSE00000866275
chr17:
26696872-26696528
345
VTNC_HUMAN
62-177
116
0
-
-
1.4
ENST00000226218
4
ENSE00000866274
chr17:
26696449-26696310
140
VTNC_HUMAN
177-223
47
0
-
-
1.5
ENST00000226218
5
ENSE00000705693
chr17:
26696049-26695893
157
VTNC_HUMAN
224-276
53
0
-
-
1.6
ENST00000226218
6
ENSE00000705695
chr17:
26695694-26695542
153
VTNC_HUMAN
276-327
52
0
-
-
1.7a
ENST00000226218
7a
ENSE00000705697
chr17:
26695080-26694736
345
VTNC_HUMAN
327-442
116
0
-
-
1.8b
ENST00000226218
8b
ENSE00001177290
chr17:
26694502-26694297
206
VTNC_HUMAN
442-478
37
0
-
-
2.1
ENST00000340093
1
ENSE00001048170
chr19:
44174502-44174218
285
UPAR_HUMAN
1-19
19
0
-
-
2.2
ENST00000340093
2
ENSE00000847438
chr19:
44171843-44171733
111
UPAR_HUMAN
19-56
38
1
U:1-34
34
2.3
ENST00000340093
3
ENSE00000494759
chr19:
44169611-44169468
144
UPAR_HUMAN
56-104
49
1
U:34-82
49
2.4
ENST00000340093
4
ENSE00000710867
chr19:
44160792-44160631
162
UPAR_HUMAN
104-158
55
1
U:82-136 (gaps)
55
2.5
ENST00000340093
5
ENSE00000710856
chr19:
44159725-44159591
135
UPAR_HUMAN
158-203
46
1
U:136-181
46
2.6
ENST00000340093
6
ENSE00000847435
chr19:
44156523-44156377
147
UPAR_HUMAN
203-252
50
1
U:181-230
50
2.7
ENST00000340093
7
ENSE00000847434
chr19:
44153295-44152732
564
UPAR_HUMAN
252-335
84
1
U:230-275
46
3.3c
ENST00000372764
3c
ENSE00001820360
chr10:
75670915-75670976
62
UROK_HUMAN
-
0
0
-
-
3.4b
ENST00000372764
4b
ENSE00002193721
chr10:
75671283-75671370
88
UROK_HUMAN
1-19
19
0
-
-
3.5
ENST00000372764
5
ENSE00001276413
chr10:
75671799-75671826
28
UROK_HUMAN
20-29
10
1
A:8-9
2
3.6a
ENST00000372764
6a
ENSE00001169210
chr10:
75671973-75672080
108
UROK_HUMAN
29-65
37
1
A:9-45
37
3.7b
ENST00000372764
7b
ENSE00001169200
chr10:
75672682-75672856
175
UROK_HUMAN
65-123
59
1
A:45-103
59
3.8
ENST00000372764
8
ENSE00000834105
chr10:
75673048-75673139
92
UROK_HUMAN
123-154
32
1
A:103-132
30
3.9b
ENST00000372764
9b
ENSE00001169184
chr10:
75673297-75673516
220
UROK_HUMAN
154-227
74
0
-
-
3.10
ENST00000372764
10
ENSE00001169178
chr10:
75673738-75673886
149
UROK_HUMAN
227-277
51
0
-
-
3.11
ENST00000372764
11
ENSE00001169173
chr10:
75674534-75674674
141
UROK_HUMAN
277-324
48
0
-
-
3.13
ENST00000372764
13
ENSE00001169164
chr10:
75675009-75675157
149
UROK_HUMAN
324-373
50
0
-
-
3.14d
ENST00000372764
14d
ENSE00001892698
chr10:
75676147-75677255
1109
UROK_HUMAN
374-431
58
0
-
-
[
close EXON info
]
SCOP Domains
(4, 6)
Info
All SCOP Domains
1a: SCOP_d3bt1a1 (A:8-49)
2a: SCOP_d3bt1a2 (A:50-132)
3a: SCOP_d3bt1u1 (U:1-86)
3b: SCOP_d3bt1u2 (U:188-275)
3c: SCOP_d3bt1u3 (U:87-187)
4a: SCOP_d3bt1b_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Small proteins
(3458)
Fold
:
Knottins (small inhibitors, toxins, lectins)
(761)
Superfamily
:
EGF/Laminin
(347)
Family
:
EGF-type module
(304)
Protein domain
:
Plasminogen activator (urokinase-type)
(6)
Human (Homo sapiens) [TaxId: 9606]
(6)
1a
d3bt1a1
A:8-49
Fold
:
Kringle-like
(68)
Superfamily
:
Kringle-like
(68)
Family
:
Kringle modules
(54)
Protein domain
:
Urokinase-type plasminogen activator
(7)
Human (Homo sapiens) [TaxId: 9606]
(7)
2a
d3bt1a2
A:50-132
Fold
:
Snake toxin-like
(152)
Superfamily
:
Snake toxin-like
(152)
Family
:
Extracellular domain of cell surface receptors
(39)
Protein domain
:
Urokinase plasminogen activator surface receptor uPAR
(5)
Human (Homo sapiens) [TaxId: 9606]
(5)
3a
d3bt1u1
U:1-86
3b
d3bt1u2
U:188-275
3c
d3bt1u3
U:87-187
Fold
:
Somatomedin B domain
(6)
Superfamily
:
Somatomedin B domain
(6)
Family
:
Somatomedin B domain
(6)
Protein domain
:
Vitronectin
(6)
Human (Homo sapiens) [TaxId: 9606]
(6)
4a
d3bt1b_
B:
[
close SCOP info
]
CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_3bt1A02 (A:50-132)
2a: CATH_3bt1A01 (A:8-49)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Plasminogen Kringle 4
(42)
Homologous Superfamily
:
Plasminogen Kringle 4
(42)
Human (Homo sapiens)
(37)
1a
3bt1A02
A:50-132
Architecture
:
Ribbon
(789)
Topology
:
Laminin
(270)
Homologous Superfamily
:
Laminin
(263)
Human (Homo sapiens)
(195)
2a
3bt1A01
A:8-49
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain U
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (78 KB)
Header - Asym.Unit
Biol.Unit 1 (71 KB)
Header - Biol.Unit 1
Biol.Unit 2 (65 KB)
Header - Biol.Unit 2
Biol.Unit 3 (9 KB)
Header - Biol.Unit 3
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
3BT1
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
