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1TYE
Biol. Unit 1
Info
Asym.Unit (441 KB)
Biol.Unit 1 (149 KB)
Biol.Unit 2 (150 KB)
Biol.Unit 3 (149 KB)
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(1)
Title
:
STRUCTURAL BASIS FOR ALLOSTERY IN INTEGRINS AND BINDING OF LIGAND-MIMETIC THERAPEUTICS TO THE PLATELET RECEPTOR FOR FIBRINOGEN
Authors
:
T. Xiao, J. Takagi, B. S. Coller, J. -H. Wang, T. A. Springer
Date
:
07 Jul 04 (Deposition) - 12 Oct 04 (Release) - 10 Sep 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Keywords
:
Crystal Structure; Platelet Integrin Alphaiibbeta3; Fibrinogen Binding; Allostery; Therapeutic Antagonism, Cell Adhesion
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Xiao, J. Takagi, B. S. Coller, J. -H. Wang, T. A. Springer
Structural Basis For Allostery In Integrins And Binding To Fibrinogen-Mimetic Therapeutics
Nature V. 432 59 2004
[
close entry info
]
Hetero Components
(4, 7)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
1c: BETA-D-MANNOSE (BMAc)
3a: CACODYLATE ION (CACa)
3b: CACODYLATE ION (CACb)
3c: CACODYLATE ION (CACc)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
3d: CALCIUM ION (CAd)
3e: CALCIUM ION (CAe)
3f: CALCIUM ION (CAf)
3g: CALCIUM ION (CAg)
3h: CALCIUM ION (CAh)
3i: CALCIUM ION (CAi)
3j: CALCIUM ION (CAj)
3k: CALCIUM ION (CAk)
3l: CALCIUM ION (CAl)
3m: CALCIUM ION (CAm)
3n: CALCIUM ION (CAn)
3o: CALCIUM ION (CAo)
3p: CALCIUM ION (CAp)
3q: CALCIUM ION (CAq)
3r: CALCIUM ION (CAr)
4a: ALPHA-D-MANNOSE (MANa)
4b: ALPHA-D-MANNOSE (MANb)
4c: ALPHA-D-MANNOSE (MANc)
4d: ALPHA-D-MANNOSE (MANd)
5a: MAGNESIUM ION (MGa)
5b: MAGNESIUM ION (MGb)
5c: MAGNESIUM ION (MGc)
6a: N-ACETYL-D-GLUCOSAMINE (NAGa)
6b: N-ACETYL-D-GLUCOSAMINE (NAGb)
6c: N-ACETYL-D-GLUCOSAMINE (NAGc)
6d: N-ACETYL-D-GLUCOSAMINE (NAGd)
6e: N-ACETYL-D-GLUCOSAMINE (NAGe)
6f: N-ACETYL-D-GLUCOSAMINE (NAGf)
6g: N-ACETYL-D-GLUCOSAMINE (NAGg)
6h: N-ACETYL-D-GLUCOSAMINE (NAGh)
6i: N-ACETYL-D-GLUCOSAMINE (NAGi)
6j: N-ACETYL-D-GLUCOSAMINE (NAGj)
6k: N-ACETYL-D-GLUCOSAMINE (NAGk)
6l: N-ACETYL-D-GLUCOSAMINE (NAGl)
6m: N-ACETYL-D-GLUCOSAMINE (NAGm)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
1
Ligand/Ion
BETA-D-MANNOSE
2
CA
-1
Ligand/Ion
CALCIUM ION
3
CAC
1
Ligand/Ion
CACODYLATE ION
4
MAN
1
Ligand/Ion
ALPHA-D-MANNOSE
5
MG
-1
Ligand/Ion
MAGNESIUM ION
6
NAG
4
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(14, 14)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: CC3 (SOFTWARE)
08: CC6 (SOFTWARE)
09: CC7 (SOFTWARE)
10: CC8 (SOFTWARE)
11: CC9 (SOFTWARE)
12: DC1 (SOFTWARE)
13: DC2 (SOFTWARE)
14: DC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN B:99 , PHE B:100
BINDING SITE FOR RESIDUE NAG B 1001
02
AC2
SOFTWARE
MET A:285 , LEU B:317 , ASN B:320 , NAG B:1003
BINDING SITE FOR RESIDUE NAG B 1002
03
AC3
SOFTWARE
ARG A:281 , NAG B:1002 , MAN B:1004
BINDING SITE FOR RESIDUE NAG B 1003
04
AC4
SOFTWARE
NAG B:1003 , BMA B:1005
BINDING SITE FOR RESIDUE MAN B 1004
05
AC5
SOFTWARE
MAN B:1004
BINDING SITE FOR RESIDUE BMA B 1005
06
AC6
SOFTWARE
SER B:369 , ASN B:371 , SER B:398 , GLU B:400
BINDING SITE FOR RESIDUE NAG B 1006
07
CC3
SOFTWARE
SER B:121 , TYR B:122 , SER B:123 , ARG B:214 , ASN B:215 , ASP B:217 , GLU B:220 , MG B:1401
BINDING SITE FOR RESIDUE CAC B 1301
08
CC6
SOFTWARE
SER B:121 , SER B:123 , GLU B:220 , CAC B:1301 , HOH B:1404 , HOH B:1405
BINDING SITE FOR RESIDUE MG B 1401
09
CC7
SOFTWARE
SER B:123 , ASP B:126 , ASP B:127 , ASP B:251 , HOH B:1406
BINDING SITE FOR RESIDUE CA B 1402
10
CC8
SOFTWARE
ASP B:158 , ASN B:215 , ASP B:217 , PRO B:219 , GLU B:220
BINDING SITE FOR RESIDUE CA B 1403
11
CC9
SOFTWARE
GLU A:243 , ASP A:245 , ASP A:247 , THR A:250 , GLU A:252
BINDING SITE FOR RESIDUE CA A 1404
12
DC1
SOFTWARE
ASP A:297 , ASN A:299 , ASP A:301 , ARG A:303 , ASP A:305
BINDING SITE FOR RESIDUE CA A 1405
13
DC2
SOFTWARE
ASP A:365 , ASP A:367 , ASP A:369 , TYR A:371 , ASP A:373
BINDING SITE FOR RESIDUE CA A 1406
14
DC3
SOFTWARE
ASP A:426 , ASP A:428 , ASN A:430 , TYR A:432 , ASP A:434
BINDING SITE FOR RESIDUE CA A 1407
[
close Site info
]
SAPs(SNPs)/Variants
(49, 49)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_014176 (T9I, chain A, )
02: VAR_003993 (L33P, chain B, )
03: VAR_069920 (C38Y, chain B, )
04: VAR_049633 (L40R, chain B, )
05: VAR_030445 (L55P, chain A, )
06: VAR_030473 (R93W, chain B, )
07: VAR_030446 (A108V, chain A, )
08: VAR_030474 (Y115C, chain B, )
09: VAR_010649 (L117W, chain B, )
10: VAR_069921 (M118R, chain B, )
11: VAR_030475 (D119N, chain B, )
12: VAR_003998 (D119Y, chain B, )
13: VAR_030476 (M124V, chain B, )
14: VAR_030447 (C130W, chain A, )
15: VAR_030477 (T140I, chain B, )
16: VAR_030448 (Y143H, chain A, )
17: VAR_003994 (R143Q, chain B, )
18: VAR_009885 (P145A, chain A, )
19: VAR_009886 (P145L, chain A, )
20: VAR_010651 (S162L, chain B, )
21: VAR_030449 (F171C, chain A, )
22: VAR_030450 (T176I, chain A, )
23: VAR_030451 (L183P, chain A, )
24: VAR_030452 (F191L, chain A, )
25: VAR_030478 (L196P, chain B, )
26: VAR_003999 (R214Q, chain B, )
27: VAR_004000 (R214W, chain B, )
28: VAR_030479 (R216Q, chain B, )
29: VAR_030480 (D217V, chain B, )
30: VAR_069922 (G221D, chain B, )
31: VAR_030453 (G236E, chain A, )
32: VAR_003979 (G242D, chain A, )
33: VAR_069923 (K253M, chain B, )
34: VAR_030481 (L262P, chain B, )
35: VAR_004001 (H280P, chain B, )
36: VAR_054820 (A282A, chain A, )
37: VAR_009887 (F289S, chain A, )
38: VAR_030482 (M295L, chain B, )
39: VAR_030454 (V298F, chain A, )
40: VAR_030483 (I304N, chain B, )
41: VAR_009888 (E324K, chain A, )
42: VAR_003980 (R327H, chain A, )
43: VAR_030455 (G349D, chain A, )
44: VAR_030456 (I374T, chain A, )
45: VAR_004002 (C374Y, chain B, )
46: VAR_030457 (G381R, chain A, )
47: VAR_003995 (P407A, chain B, )
48: VAR_003981 (G418D, chain A, )
49: VAR_014178 (V427I, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_014176
T
40
I
ITA2B_HUMAN
Polymorphism
5915
A
T
9
I
02
UniProt
VAR_003993
L
59
P
ITB3_HUMAN
Polymorphism
5918
B
L
33
P
03
UniProt
VAR_069920
C
64
Y
ITB3_HUMAN
Disease (GT)
---
B
C
38
Y
04
UniProt
VAR_049633
L
66
R
ITB3_HUMAN
Polymorphism
36080296
B
L
40
R
05
UniProt
VAR_030445
L
86
P
ITA2B_HUMAN
Disease (GT)
---
A
L
55
P
06
UniProt
VAR_030473
R
119
W
ITB3_HUMAN
Disease (GT)
---
B
R
93
W
07
UniProt
VAR_030446
A
139
V
ITA2B_HUMAN
Disease (GT)
---
A
A
108
V
08
UniProt
VAR_030474
Y
141
C
ITB3_HUMAN
Disease (GT)
---
B
Y
115
C
09
UniProt
VAR_010649
L
143
W
ITB3_HUMAN
Disease (GT)
---
B
L
117
W
10
UniProt
VAR_069921
M
144
R
ITB3_HUMAN
Disease (GT)
---
B
M
118
R
11
UniProt
VAR_030475
D
145
N
ITB3_HUMAN
Disease (GT)
---
B
D
119
N
12
UniProt
VAR_003998
D
145
Y
ITB3_HUMAN
Disease (GT)
---
B
D
119
Y
13
UniProt
VAR_030476
M
150
V
ITB3_HUMAN
Disease (GT)
---
B
M
124
V
14
UniProt
VAR_030447
C
161
W
ITA2B_HUMAN
Disease (GT)
---
A
C
130
W
15
UniProt
VAR_030477
T
166
I
ITB3_HUMAN
Unclassified
---
B
T
140
I
16
UniProt
VAR_030448
Y
174
H
ITA2B_HUMAN
Disease (GT)
---
A
Y
143
H
17
UniProt
VAR_003994
R
169
Q
ITB3_HUMAN
Polymorphism
5917
B
R
143
Q
18
UniProt
VAR_009885
P
176
A
ITA2B_HUMAN
Disease (GT)
---
A
P
145
A
19
UniProt
VAR_009886
P
176
L
ITA2B_HUMAN
Disease (GT)
---
A
P
145
L
20
UniProt
VAR_010651
S
188
L
ITB3_HUMAN
Disease (GT)
---
B
S
162
L
21
UniProt
VAR_030449
F
202
C
ITA2B_HUMAN
Disease (GT)
---
A
F
171
C
22
UniProt
VAR_030450
T
207
I
ITA2B_HUMAN
Disease (GT)
---
A
T
176
I
23
UniProt
VAR_030451
L
214
P
ITA2B_HUMAN
Disease (GT)
---
A
L
183
P
24
UniProt
VAR_030452
F
222
L
ITA2B_HUMAN
Disease (GT)
---
A
F
191
L
25
UniProt
VAR_030478
L
222
P
ITB3_HUMAN
Disease (GT)
---
B
L
196
P
26
UniProt
VAR_003999
R
240
Q
ITB3_HUMAN
Disease (GT)
---
B
R
214
Q
27
UniProt
VAR_004000
R
240
W
ITB3_HUMAN
Disease (GT)
---
B
R
214
W
28
UniProt
VAR_030479
R
242
Q
ITB3_HUMAN
Disease (GT)
---
B
R
216
Q
29
UniProt
VAR_030480
D
243
V
ITB3_HUMAN
Disease (GT)
---
B
D
217
V
30
UniProt
VAR_069922
G
247
D
ITB3_HUMAN
Disease (GT)
---
B
G
221
D
31
UniProt
VAR_030453
G
267
E
ITA2B_HUMAN
Disease (GT)
---
A
G
236
E
32
UniProt
VAR_003979
G
273
D
ITA2B_HUMAN
Disease (GT)
---
A
G
242
D
33
UniProt
VAR_069923
K
279
M
ITB3_HUMAN
Disease (GT)
---
B
K
253
M
34
UniProt
VAR_030481
L
288
P
ITB3_HUMAN
Disease (GT)
---
B
L
262
P
35
UniProt
VAR_004001
H
306
P
ITB3_HUMAN
Disease (GT)
13306476
B
H
280
P
36
UniProt
VAR_054820
G
313
A
ITA2B_HUMAN
Polymorphism
1126554
A
A
282
A
37
UniProt
VAR_009887
F
320
S
ITA2B_HUMAN
Disease (GT)
---
A
F
289
S
38
UniProt
VAR_030482
M
321
L
ITB3_HUMAN
Disease (GT)
---
B
M
295
L
39
UniProt
VAR_030454
V
329
F
ITA2B_HUMAN
Disease (GT)
---
A
V
298
F
40
UniProt
VAR_030483
I
330
N
ITB3_HUMAN
Disease (GT)
---
B
I
304
N
41
UniProt
VAR_009888
E
355
K
ITA2B_HUMAN
Disease (GT)
---
A
E
324
K
42
UniProt
VAR_003980
R
358
H
ITA2B_HUMAN
Disease (GT)
---
A
R
327
H
43
UniProt
VAR_030455
G
380
D
ITA2B_HUMAN
Disease (GT)
---
A
G
349
D
44
UniProt
VAR_030456
I
405
T
ITA2B_HUMAN
Disease (GT)
---
A
I
374
T
45
UniProt
VAR_004002
C
400
Y
ITB3_HUMAN
Disease (GT)
---
B
C
374
Y
46
UniProt
VAR_030457
G
412
R
ITA2B_HUMAN
Disease (GT)
---
A
G
381
R
47
UniProt
VAR_003995
P
433
A
ITB3_HUMAN
Polymorphism
121918448
B
P
407
A
48
UniProt
VAR_003981
G
449
D
ITA2B_HUMAN
Disease (GT)
---
A
G
418
D
49
UniProt
VAR_014178
V
453
I
ITB3_HUMAN
Polymorphism
5921
B
V
427
I
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 7)
Info
All PROSITE Patterns/Profiles
1: FG_GAP (A:4-65,A:79-142,A:156-207,A:275-34...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FG_GAP
PS51470
FG-GAP repeat profile.
ITA2B_HUMAN
35-96
110-173
187-238
306-371
251-305
373-432
435-496
7
A:4-65
-
-
A:79-142
-
-
A:156-207
-
-
A:275-340
-
-
A:220-274
-
-
A:342-401
-
-
A:404-452
-
-
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
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
(4, 12)
Info
All SCOP Domains
1a: SCOP_d1tyea_ (A:)
1b: SCOP_d1tyec_ (C:)
1c: SCOP_d1tyee_ (E:)
2a: SCOP_d1tyeb1 (B:58-106,B:355-440)
2b: SCOP_d1tyed1 (D:58-106,D:355-440)
2c: SCOP_d1tyef1 (F:58-106,F:355-440)
3a: SCOP_d1tyeb2 (B:107-354)
3b: SCOP_d1tyed2 (D:107-354)
3c: SCOP_d1tyef2 (F:107-354)
4a: SCOP_d1tyeb3 (B:1-57)
4b: SCOP_d1tyed3 (D:1-57)
4c: SCOP_d1tyef3 (F:1-57)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
7-bladed beta-propeller
(245)
Superfamily
:
Integrin alpha N-terminal domain
(24)
Family
:
Integrin alpha N-terminal domain
(23)
Protein domain
:
Integrin alpha N-terminal domain
(21)
Human (Homo sapiens), isoform IIb [TaxId: 9606]
(17)
1a
d1tyea_
A:
1b
d1tyec_
C:
1c
d1tyee_
E:
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Integrin domains
(12)
Family
:
Integrin domains
(9)
Protein domain
:
Hybrid domain of integrin beta
(5)
Human (Homo sapiens) [TaxId: 9606]
(5)
2a
d1tyeb1
B:58-106,B:355-440
2b
d1tyed1
D:58-106,D:355-440
2c
d1tyef1
F:58-106,F:355-440
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
vWA-like
(111)
Superfamily
:
vWA-like
(111)
Family
:
Integrin A (or I) domain
(84)
Protein domain
:
Integrin beta A domain
(5)
Human (Homo sapiens) [TaxId: 9606]
(5)
3a
d1tyeb2
B:107-354
3b
d1tyed2
D:107-354
3c
d1tyef2
F:107-354
Class
:
Small proteins
(3458)
Fold
:
Trefoil/Plexin domain-like
(15)
Superfamily
:
Plexin repeat
(6)
Family
:
Plexin repeat
(6)
Protein domain
:
Integrin beta-3
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
4a
d1tyeb3
B:1-57
4b
d1tyed3
D:1-57
4c
d1tyef3
F:1-57
[
close SCOP info
]
CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_1tyeB03 (B:107-353)
1b: CATH_1tyeD03 (D:107-353)
1c: CATH_1tyeF03 (F:107-353)
2a: CATH_1tyeA00 (A:1-452)
2b: CATH_1tyeC00 (C:1-452)
2c: CATH_1tyeE00 (E:1-452)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.410, no name defined]
(87)
Human (Homo sapiens)
(66)
1a
1tyeB03
B:107-353
1b
1tyeD03
D:107-353
1c
1tyeF03
F:107-353
Class
:
Mainly Beta
(13760)
Architecture
:
7 Propellor
(136)
Topology
:
Methylamine Dehydrogenase; Chain H
(136)
Homologous Superfamily
:
Integrin alpha N-terminal domain, Chain A
(15)
Human (Homo sapiens)
(15)
2a
1tyeA00
A:1-452
2b
1tyeC00
C:1-452
2c
1tyeE00
E:1-452
[
close CATH info
]
Pfam Domains
(3, 9)
Info
all PFAM domains
1a: PFAM_FG_GAP_1tyeE01 (E:289-331)
1b: PFAM_FG_GAP_1tyeE02 (E:289-331)
1c: PFAM_FG_GAP_1tyeE03 (E:289-331)
2a: PFAM_Integrin_alpha2_1tyeE04 (E:450-452)
2b: PFAM_Integrin_alpha2_1tyeE05 (E:450-452)
2c: PFAM_Integrin_alpha2_1tyeE06 (E:450-452)
3a: PFAM_Integrin_beta_1tyeF01 (F:12-435)
3b: PFAM_Integrin_beta_1tyeF02 (F:12-435)
3c: PFAM_Integrin_beta_1tyeF03 (F:12-435)
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Clan
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Beta_propeller
(192)
Family
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FG-GAP
(14)
Homo sapiens (Human)
(14)
1a
FG-GAP-1tyeE01
E:289-331
1b
FG-GAP-1tyeE02
E:289-331
1c
FG-GAP-1tyeE03
E:289-331
Clan
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E-set
(290)
Family
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Integrin_alpha2
(14)
Homo sapiens (Human)
(14)
2a
Integrin_alpha2-1tyeE04
E:450-452
2b
Integrin_alpha2-1tyeE05
E:450-452
2c
Integrin_alpha2-1tyeE06
E:450-452
Clan
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no clan defined [family: Integrin_beta]
(18)
Family
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Integrin_beta
(18)
Homo sapiens (Human)
(18)
3a
Integrin_beta-1tyeF01
F:12-435
3b
Integrin_beta-1tyeF02
F:12-435
3c
Integrin_beta-1tyeF03
F:12-435
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