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Getting 'Biological Unit' information from database.
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Getting 'Hetero Component' information from database.
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Getting 'Site' information from database.
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Getting 'PROSITE' information from database.
3NID
Biol. Unit 1
Info
Asym.Unit (928 KB)
Biol.Unit 1 (463 KB)
Biol.Unit 2 (457 KB)
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(1)
Title
:
THE CLOSED HEADPIECE OF INTEGRIN ALPHAIIB BETA3 AND ITS COMPLEX WITH AN ALPAHIIB BETA3 -SPECIFIC ANTAGONIST THAT DOES NOT INDUCE OPENING
Authors
:
J. H. Zhu, J. Q. Zhu, T. A. Springer
Date
:
15 Jun 10 (Deposition) - 22 Dec 10 (Release) - 22 Dec 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D,E,F,H,L
Biol. Unit 1: A,B,H,L (1x)
Biol. Unit 2: C,D,E,F (1x)
Keywords
:
Integrin, Headpiece, Alphaiib, Beta3, Cell Adhesion-Blood Clotting Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. H. Zhu, J. Q. Zhu, A. Negri, D. Provasi, M. Filizola, B. S. Coller, T. A. Springer
Closed Headpiece Of Integrin {Alpha}Iib{Beta}3 And Its Complex With An {Alpha}Iib{Beta}3-Specific Antagonist That Does Not Induce Opening.
Blood V. 116 5050 2010
[
close entry info
]
Hetero Components
(4, 19)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
1g: CALCIUM ION (CAg)
1h: CALCIUM ION (CAh)
1i: CALCIUM ION (CAi)
1j: CALCIUM ION (CAj)
1k: CALCIUM ION (CAk)
1l: CALCIUM ION (CAl)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
2i: GLYCEROL (GOLi)
3a: ALPHA-D-MANNOSE (MANa)
3b: ALPHA-D-MANNOSE (MANb)
3c: ALPHA-D-MANNOSE (MANc)
3d: ALPHA-D-MANNOSE (MANd)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
5a: N-ACETYL-D-GLUCOSAMINE (NAGa)
5b: N-ACETYL-D-GLUCOSAMINE (NAGb)
5c: N-ACETYL-D-GLUCOSAMINE (NAGc)
5d: N-ACETYL-D-GLUCOSAMINE (NAGd)
5e: N-ACETYL-D-GLUCOSAMINE (NAGe)
5f: N-ACETYL-D-GLUCOSAMINE (NAGf)
5g: N-ACETYL-D-GLUCOSAMINE (NAGg)
5h: N-ACETYL-D-GLUCOSAMINE (NAGh)
5i: N-ACETYL-D-GLUCOSAMINE (NAGi)
5j: N-ACETYL-D-GLUCOSAMINE (NAGj)
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)
6i: SULFATE ION (SO4i)
6j: SULFATE ION (SO4j)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
GOL
7
Ligand/Ion
GLYCEROL
3
MAN
3
Ligand/Ion
ALPHA-D-MANNOSE
4
MG
-1
Ligand/Ion
MAGNESIUM ION
5
NAG
5
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
6
SO4
4
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(28, 28)
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: DC4 (SOFTWARE)
26: EC9 (SOFTWARE)
27: FC1 (SOFTWARE)
28: FC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:243 , ASP A:245 , ASP A:247 , THR A:250 , GLU A:252
BINDING SITE FOR RESIDUE CA A 2004
02
AC2
SOFTWARE
ASP A:297 , ASN A:299 , ASP A:301 , ARG A:303 , ASP A:305 , HOH A:471
BINDING SITE FOR RESIDUE CA A 2005
03
AC3
SOFTWARE
ASP A:365 , ASP A:367 , ASP A:369 , TYR A:371 , ASP A:373 , HOH A:470
BINDING SITE FOR RESIDUE CA A 2006
04
AC4
SOFTWARE
ASP A:426 , ASP A:428 , ASN A:430 , TYR A:432 , ASP A:434 , HOH A:472
BINDING SITE FOR RESIDUE CA A 2007
05
AC5
SOFTWARE
GLN A:395 , SER A:401 , ARG A:402 , HOH A:595 , HOH A:632
BINDING SITE FOR RESIDUE GOL A 458
06
AC6
SOFTWARE
PHE A:160 , TYR A:190 , GOL A:462 , HOH A:644 , HOH A:874 , HOH A:875
BINDING SITE FOR RESIDUE GOL A 459
07
AC7
SOFTWARE
LEU A:1 , LEU A:3 , GLN A:405 , PRO C:403 , HOH C:635
BINDING SITE FOR RESIDUE GOL A 460
08
AC8
SOFTWARE
ALA A:89 , ARG A:90 , HIS A:112 , LYS A:124 , HOH A:643 , HOH A:845
BINDING SITE FOR RESIDUE GOL A 461
09
AC9
SOFTWARE
TYR A:190 , LEU A:192 , PHE A:231 , GOL A:459 , HOH A:487 , HOH A:489 , HOH A:575 , HOH A:644 , HOH A:874
BINDING SITE FOR RESIDUE GOL A 462
10
BC1
SOFTWARE
PRO A:403 , HOH A:697 , LEU C:1 , ASN C:2 , LEU C:3
BINDING SITE FOR RESIDUE GOL A 463
11
BC2
SOFTWARE
ILE A:154 , TYR A:155 , ASN A:158 , SER A:161
BINDING SITE FOR RESIDUE SO4 A 464
12
BC3
SOFTWARE
SER B:121 , GLU B:220 , HOH B:492 , HOH B:493 , HOH B:494 , HOH B:495
BINDING SITE FOR RESIDUE MG B 2001
13
BC4
SOFTWARE
SER B:123 , ASP B:126 , ASP B:127 , MET B:335 , HOH B:474 , HOH B:475
BINDING SITE FOR RESIDUE CA B 2002
14
BC5
SOFTWARE
ASP B:158 , ASN B:215 , ASP B:217 , PRO B:219 , GLU B:220
BINDING SITE FOR RESIDUE CA B 2003
15
BC6
SOFTWARE
LYS B:98 , ASN B:99 , PHE B:100 , HOH B:539
BINDING SITE FOR RESIDUE NAG B 3099
16
BC7
SOFTWARE
MET A:285 , LEU B:317 , ASN B:320 , HOH B:509 , HOH B:547 , HOH B:575 , HOH B:763 , HOH B:950 , NAG B:3321
BINDING SITE FOR RESIDUE NAG B 3320
17
BC8
SOFTWARE
ARG A:281 , HOH B:950 , HOH B:951 , HOH B:952 , NAG B:3320 , MAN B:3322 , MAN B:3323
BINDING SITE FOR RESIDUE NAG B 3321
18
BC9
SOFTWARE
NAG B:3321 , MAN B:3323 , MAN B:3324
BINDING SITE FOR RESIDUE MAN B 3322
19
CC1
SOFTWARE
ARG A:281 , NAG B:3321 , MAN B:3322
BINDING SITE FOR RESIDUE MAN B 3323
20
CC2
SOFTWARE
MAN B:3322
BINDING SITE FOR RESIDUE MAN B 3324
21
CC3
SOFTWARE
SER B:369 , ASN B:371 , SER B:398 , GLU B:400 , NAG B:3372
BINDING SITE FOR RESIDUE NAG B 3371
22
CC4
SOFTWARE
NAG B:3371
BINDING SITE FOR RESIDUE NAG B 3372
23
CC5
SOFTWARE
SER B:300 , ASN B:303 , ILE B:304 , PRO B:326 , HOH B:783
BINDING SITE FOR RESIDUE GOL B 472
24
CC6
SOFTWARE
GLN B:82 , GLN B:106 , SER B:243 , ARG B:352 , GLY B:420 , PHE B:421
BINDING SITE FOR RESIDUE SO4 B 473
25
DC4
SOFTWARE
PHE A:10 , PHE A:411 , GLN A:444 , PRO C:383
BINDING SITE FOR RESIDUE SO4 C 460
26
EC9
SOFTWARE
GLN A:134 , SER A:137 , ARG D:461 , CYS D:462
BINDING SITE FOR RESIDUE SO4 D 473
27
FC1
SOFTWARE
LYS H:38 , ARG H:40 , GLU H:46 , PHE H:64
BINDING SITE FOR RESIDUE SO4 H 222
28
FC2
SOFTWARE
GLN L:37 , LYS L:39 , LEU L:47 , PRO L:59 , PHE L:62
BINDING SITE FOR RESIDUE SO4 L 215
[
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 (G282A, 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
G
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
(3, 9)
Info
All PROSITE Patterns/Profiles
1: FG_GAP (A:4-65,A:79-142,A:156-207,A:275-34...)
2: EGF_1 (B:460-466)
3: EGF_2 (B:460-466)
;
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:404-454
-
2
EGF_1
PS00022
EGF-like domain signature 1.
ITB3_HUMAN
486-497
573-584
1
B:460-466
-
-
3
EGF_2
PS01186
EGF-like domain signature 2.
ITB3_HUMAN
486-499
1
B:460-466
-
[
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
(3, 6)
Info
All SCOP Domains
1a: SCOP_d3nida_ (A:)
1b: SCOP_d3nidc_ (C:)
2a: SCOP_d3nidf1 (F:1-107)
2b: SCOP_d3nidl1 (L:1-107)
3a: SCOP_d3nidf2 (F:108-214)
3b: SCOP_d3nidl2 (L:108-214)
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
d3nida_
A:
1b
d3nidc_
C:
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
automated matches
(864)
Protein domain
:
automated matches
(864)
Mouse (Mus musculus) [TaxId: 10090]
(360)
2a
d3nidf1
F:1-107
2b
d3nidl1
L:1-107
Family
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
automated matches
(652)
Mouse (Mus musculus) [TaxId: 10090]
(309)
3a
d3nidf2
F:108-214
3b
d3nidl2
L:108-214
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Asymmetric Unit 1
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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Asym.Unit (928 KB)
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Biol.Unit 1 (463 KB)
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