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4DPG
Asym. Unit
Info
Asym.Unit (1.4 MB)
Biol.Unit 1 (350 KB)
Biol.Unit 2 (350 KB)
Biol.Unit 3 (352 KB)
Biol.Unit 4 (352 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN LYSRS: P38/AIMP2 COMPLEX I
Authors
:
P. Fang, J. Wang, S. P. Bennett, M. Guo
Date
:
13 Feb 12 (Deposition) - 13 Feb 13 (Release) - 13 Feb 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.84
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,I (1x)
Biol. Unit 2: C,D,K (1x)
Biol. Unit 3: E,F,L (1x)
Biol. Unit 4: G,H,J (1x)
Keywords
:
Lysyl-Trna Synthetase, Lysrs, P38, Aimp2, Multi Trna Synthetase Complex Sub-Complex, Ligase-Apoptosis Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Ofir-Birin, P. Fang, S. P. Bennett, H. M. Zhang, J. Wang, I. Rachmin, R. Shapiro, J. Song, A. Dagan, J. Pozo, S. Kim, A. G. Marshall, P. Schimmel, X. L. Yang, H. Nechushtan, E. Razin, M. Guo
Structural Switch Of Lysyl-Trna Synthetase Between Translation And Transcription.
Mol. Cell V. 49 30 2013
[
close entry info
]
Hetero Components
(4, 29)
Info
All Hetero Components
1a: ALANINE (ALAa)
2a: DIPHOSPHOMETHYLPHOSPHONIC ACID ADE... (APCa)
2b: DIPHOSPHOMETHYLPHOSPHONIC ACID ADE... (APCb)
2c: DIPHOSPHOMETHYLPHOSPHONIC ACID ADE... (APCc)
2d: DIPHOSPHOMETHYLPHOSPHONIC ACID ADE... (APCd)
2e: DIPHOSPHOMETHYLPHOSPHONIC ACID ADE... (APCe)
2f: DIPHOSPHOMETHYLPHOSPHONIC ACID ADE... (APCf)
2g: DIPHOSPHOMETHYLPHOSPHONIC ACID ADE... (APCg)
2h: DIPHOSPHOMETHYLPHOSPHONIC ACID ADE... (APCh)
3a: LYSINE (LYSa)
3b: LYSINE (LYSb)
3c: LYSINE (LYSc)
3d: LYSINE (LYSd)
3e: LYSINE (LYSe)
3f: LYSINE (LYSf)
3g: LYSINE (LYSg)
3h: LYSINE (LYSh)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
4d: MAGNESIUM ION (MGd)
4e: MAGNESIUM ION (MGe)
4f: MAGNESIUM ION (MGf)
4g: MAGNESIUM ION (MGg)
4h: MAGNESIUM ION (MGh)
4i: MAGNESIUM ION (MGi)
4j: MAGNESIUM ION (MGj)
4k: MAGNESIUM ION (MGk)
4l: MAGNESIUM ION (MGl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ALA
1
Mod. Amino Acid
ALANINE
2
APC
8
Ligand/Ion
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
3
LYS
8
Mod. Amino Acid
LYSINE
4
MG
12
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(29, 29)
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: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:277 , ALA A:278 , ALA A:299 , GLU A:301 , GLU A:339 , TYR A:341 , ASN A:497 , TYR A:499 , GLU A:501 , GLY A:546 , TRP A:547
BINDING SITE FOR RESIDUE LYS A 601
02
AC2
SOFTWARE
ARG A:323 , THR A:330 , HIS A:331 , ASN A:332 , PHE A:335 , GLU A:494 , GLY A:550 , ARG A:553 , ILE A:564 , HOH A:721
BINDING SITE FOR RESIDUE APC A 602
03
AC3
SOFTWARE
GLU A:487 , GLU A:494
BINDING SITE FOR RESIDUE MG A 603
04
AC4
SOFTWARE
GLY B:277 , ALA B:278 , ALA B:299 , GLU B:301 , GLU B:339 , TYR B:341 , ASN B:497 , TYR B:499 , GLU B:501 , GLY B:546 , HOH B:766
BINDING SITE FOR RESIDUE LYS B 601
05
AC5
SOFTWARE
ARG B:323 , THR B:330 , HIS B:331 , ASN B:332 , PHE B:335 , ASP B:445 , GLU B:494 , ARG B:553 , ILE B:564 , MG B:603
BINDING SITE FOR RESIDUE APC B 602
06
AC6
SOFTWARE
GLU B:487 , GLU B:494 , APC B:602
BINDING SITE FOR RESIDUE MG B 603
07
AC7
SOFTWARE
GLY C:277 , ALA C:278 , ALA C:299 , GLU C:301 , GLU C:339 , TYR C:341 , ASN C:497 , TYR C:499 , GLU C:501 , GLY C:546 , TRP C:547 , HOH C:725
BINDING SITE FOR RESIDUE LYS C 601
08
AC8
SOFTWARE
ARG C:323 , THR C:330 , HIS C:331 , ASN C:332 , PHE C:335 , GLU C:494 , GLY C:550 , ARG C:553 , ILE C:564 , HOH C:744
BINDING SITE FOR RESIDUE APC C 602
09
AC9
SOFTWARE
GLU C:487 , GLU C:494
BINDING SITE FOR RESIDUE MG C 603
10
BC1
SOFTWARE
GLY D:277 , ALA D:278 , ALA D:299 , GLU D:301 , GLU D:339 , TYR D:341 , ASN D:497 , TYR D:499 , GLU D:501 , GLY D:546 , TRP D:547
BINDING SITE FOR RESIDUE LYS D 601
11
BC2
SOFTWARE
ARG D:323 , THR D:330 , HIS D:331 , ASN D:332 , PHE D:335 , ASP D:445 , GLU D:494 , ARG D:553 , ILE D:564 , MG D:603
BINDING SITE FOR RESIDUE APC D 602
12
BC3
SOFTWARE
ARG D:485 , GLU D:487 , GLU D:494 , APC D:602
BINDING SITE FOR RESIDUE MG D 603
13
BC4
SOFTWARE
GLY E:277 , ALA E:278 , ALA E:299 , GLU E:301 , GLU E:339 , TYR E:341 , ASN E:497 , TYR E:499 , GLU E:501 , GLY E:546 , TRP E:547
BINDING SITE FOR RESIDUE LYS E 601
14
BC5
SOFTWARE
ARG E:323 , THR E:330 , HIS E:331 , ASN E:332 , PHE E:335 , GLU E:494 , GLY E:550 , ARG E:553 , ILE E:564 , HOH E:718 , HOH E:734
BINDING SITE FOR RESIDUE APC E 602
15
BC6
SOFTWARE
GLU E:487 , GLU E:494
BINDING SITE FOR RESIDUE MG E 603
16
BC7
SOFTWARE
GLY F:277 , ALA F:278 , ALA F:299 , GLU F:301 , GLU F:339 , TYR F:341 , ASN F:497 , TYR F:499 , GLU F:501 , GLY F:546
BINDING SITE FOR RESIDUE LYS F 601
17
BC8
SOFTWARE
ARG F:323 , THR F:330 , HIS F:331 , ASN F:332 , PHE F:335 , ASP F:445 , GLU F:494 , ARG F:553 , ILE F:564 , MG F:603 , HOH F:713
BINDING SITE FOR RESIDUE APC F 602
18
BC9
SOFTWARE
GLU F:487 , GLU F:494 , APC F:602
BINDING SITE FOR RESIDUE MG F 603
19
CC1
SOFTWARE
HIS C:100 , HIS F:215 , HIS F:217 , PRO K:2
BINDING SITE FOR RESIDUE MG F 604
20
CC2
SOFTWARE
GLY G:277 , ALA G:278 , ALA G:299 , GLU G:301 , GLU G:339 , TYR G:341 , ASN G:497 , TYR G:499 , GLU G:501 , GLY G:546 , TRP G:547 , HOH G:738
BINDING SITE FOR RESIDUE LYS G 601
21
CC3
SOFTWARE
ARG G:323 , THR G:330 , HIS G:331 , ASN G:332 , PHE G:335 , GLU G:494 , GLY G:550 , ARG G:553 , ILE G:564 , MG G:603 , HOH G:739
BINDING SITE FOR RESIDUE APC G 602
22
CC4
SOFTWARE
GLU G:487 , GLU G:494 , APC G:602
BINDING SITE FOR RESIDUE MG G 603
23
CC5
SOFTWARE
PRO H:575
BINDING SITE FOR RESIDUE ALA H 601
24
CC6
SOFTWARE
GLY H:277 , ALA H:278 , ALA H:299 , GLU H:301 , GLU H:339 , TYR H:341 , ASN H:497 , TYR H:499 , GLU H:501 , GLY H:546
BINDING SITE FOR RESIDUE LYS H 602
25
CC7
SOFTWARE
ARG H:323 , THR H:330 , HIS H:331 , ASN H:332 , PHE H:335 , ASP H:445 , GLU H:494 , ARG H:553 , ILE H:564 , MG H:604 , HOH H:707
BINDING SITE FOR RESIDUE APC H 603
26
CC8
SOFTWARE
GLU H:487 , GLU H:494 , APC H:603
BINDING SITE FOR RESIDUE MG H 604
27
CC9
SOFTWARE
HIS A:100 , HIS H:215 , HIS H:217 , PRO I:2
BINDING SITE FOR RESIDUE MG H 605
28
DC1
SOFTWARE
HIS B:215 , HIS B:217 , HIS G:100 , PRO J:2
BINDING SITE FOR RESIDUE MG J 101
29
DC2
SOFTWARE
HIS D:215 , HIS D:217 , HIS E:100 , PRO L:2
BINDING SITE FOR RESIDUE MG L 101
[
close Site info
]
SAPs(SNPs)/Variants
(5, 40)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_064911 (L105H, chain A/B/C/D/E/F/G/H, )
2: VAR_070233 (Y145H, chain A/B/C/D/E/F/G/H, )
3: VAR_052640 (G179A, chain A/B/C/D/E/F/G/H, )
4: VAR_064912 (I274M, chain A/B/C/D/E/F/G/H, )
5: VAR_070234 (D349N, chain A/B/C/D/E/F/G/H, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_064911
L
105
H
SYK_HUMAN
Disease (CMTRIB)
---
A/B/C/D/E/F/G/H
L
105
H
2
UniProt
VAR_070233
Y
145
H
SYK_HUMAN
Disease (DFNB89)
---
A/B/C/D/E/F/G/H
Y
145
H
3
UniProt
VAR_052640
G
179
A
SYK_HUMAN
Polymorphism
11557665
A/B/C/D/E/F/G/H
G
179
A
4
UniProt
VAR_064912
I
274
M
SYK_HUMAN
Disease (CMTRIB)
---
A/B/C/D/E/F/G/H
I
274
M
5
UniProt
VAR_070234
D
349
N
SYK_HUMAN
Disease (DFNB89)
---
A/B/C/D/E/F/G/H
D
349
N
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(13, 104)
Info
All Exons
Exon 1.3 (A:71-74 | B:71-74 | C:71-74 | D:71...)
Exon 1.4b (A:75-130 | B:75-130 | C:75-130 | D...)
Exon 1.5 (A:130-161 | B:130-161 | C:130-161 ...)
Exon 1.6a (A:161-223 (gaps) | B:161-223 | C:1...)
Exon 1.7 (A:224-265 | B:224-265 | C:224-265 ...)
Exon 1.8 (A:266-305 | B:266-305 | C:266-305 ...)
Exon 1.9 (A:306-360 | B:306-360 | C:306-360 ...)
Exon 1.10b (A:360-418 | B:360-418 | C:360-418 ...)
Exon 1.11 (A:418-446 | B:418-446 | C:418-446 ...)
Exon 1.12 (A:447-475 | B:447-475 | C:447-475 ...)
Exon 1.13 (A:475-517 | B:475-517 | C:475-517 ...)
Exon 1.14 (A:518-565 | B:518-565 | C:518-565 ...)
Exon 1.15b (A:566-601 (gaps) | B:566-601 | C:5...)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.1a/1.3
02: Boundary 1.3/1.4b
03: Boundary 1.4b/1.5
04: Boundary 1.5/1.6a
05: Boundary 1.6a/1.7
06: Boundary 1.7/1.8
07: Boundary 1.8/1.9
08: Boundary 1.9/1.10b
09: Boundary 1.10b/1.11
10: Boundary 1.11/1.12
11: Boundary 1.12/1.13
12: Boundary 1.13/1.14
13: Boundary 1.14/1.15b
14: Boundary 1.15b/-
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
1.1a
ENST00000302445
1a
ENSE00001844980
chr16:
75681577-75681476
102
SYK_HUMAN
1-21
21
0
-
-
1.3
ENST00000302445
3
ENSE00001143107
chr16:
75675621-75675462
160
SYK_HUMAN
21-74
54
8
A:71-74
B:71-74
C:71-74
D:71-74
E:72-74
F:71-74
G:72-74
H:71-74
4
4
4
4
3
4
3
4
1.4b
ENST00000302445
4b
ENSE00001107190
chr16:
75674247-75674082
166
SYK_HUMAN
75-130
56
8
A:75-130
B:75-130
C:75-130
D:75-130
E:75-130
F:75-130
G:75-130
H:75-130
56
56
56
56
56
56
56
56
1.5
ENST00000302445
5
ENSE00001107188
chr16:
75670445-75670352
94
SYK_HUMAN
130-161
32
8
A:130-161
B:130-161
C:130-161
D:130-161
E:130-161
F:130-161
G:130-161
H:130-161
32
32
32
32
32
32
32
32
1.6a
ENST00000302445
6a
ENSE00001107162
chr16:
75669996-75669810
187
SYK_HUMAN
161-223
63
8
A:161-223 (gaps)
B:161-223
C:161-223 (gaps)
D:161-223
E:161-223 (gaps)
F:161-223
G:161-223 (gaps)
H:161-223
63
63
63
63
63
63
63
63
1.7
ENST00000302445
7
ENSE00001107185
chr16:
75669703-75669578
126
SYK_HUMAN
224-265
42
8
A:224-265
B:224-265
C:224-265
D:224-265
E:224-265
F:224-265
G:224-265
H:224-265
42
42
42
42
42
42
42
42
1.8
ENST00000302445
8
ENSE00001107173
chr16:
75668190-75668071
120
SYK_HUMAN
266-305
40
8
A:266-305
B:266-305
C:266-305
D:266-305
E:266-305
F:266-305
G:266-305
H:266-305
40
40
40
40
40
40
40
40
1.9
ENST00000302445
9
ENSE00001107193
chr16:
75665753-75665591
163
SYK_HUMAN
306-360
55
8
A:306-360
B:306-360
C:306-360
D:306-360
E:306-360
F:306-360
G:306-360
H:306-360
55
55
55
55
55
55
55
55
1.10b
ENST00000302445
10b
ENSE00001107182
chr16:
75665487-75665314
174
SYK_HUMAN
360-418
59
8
A:360-418
B:360-418
C:360-418
D:360-418
E:360-418
F:360-418
G:360-418
H:360-418
59
59
59
59
59
59
59
59
1.11
ENST00000302445
11
ENSE00001107180
chr16:
75665151-75665066
86
SYK_HUMAN
418-446
29
8
A:418-446
B:418-446
C:418-446
D:418-446
E:418-446
F:418-446
G:418-446
H:418-446
29
29
29
29
29
29
29
29
1.12
ENST00000302445
12
ENSE00001107178
chr16:
75664406-75664321
86
SYK_HUMAN
447-475
29
8
A:447-475
B:447-475
C:447-475
D:447-475
E:447-475
F:447-475
G:447-475
H:447-475
29
29
29
29
29
29
29
29
1.13
ENST00000302445
13
ENSE00001107196
chr16:
75663439-75663313
127
SYK_HUMAN
475-517
43
8
A:475-517
B:475-517
C:475-517
D:475-517
E:475-517
F:475-517
G:475-517
H:475-517
43
43
43
43
43
43
43
43
1.14
ENST00000302445
14
ENSE00001107165
chr16:
75662610-75662467
144
SYK_HUMAN
518-565
48
8
A:518-565
B:518-565
C:518-565
D:518-565
E:518-565
F:518-565
G:518-565
H:518-565
48
48
48
48
48
48
48
48
1.15b
ENST00000302445
15b
ENSE00001900311
chr16:
75661891-75661622
270
SYK_HUMAN
566-597
32
8
A:566-601 (gaps)
B:566-601
C:566-601
D:566-601
E:566-601
F:566-601
G:566-601
H:566-602
13
12
11
11
11
11
11
12
[
close EXON info
]
SCOP Domains
(2, 16)
Info
All SCOP Domains
1a: SCOP_d4dpga1 (A:71-221)
1b: SCOP_d4dpgc1 (C:71-221)
1c: SCOP_d4dpgd1 (D:71-221)
1d: SCOP_d4dpge1 (E:72-221)
1e: SCOP_d4dpgf1 (F:71-221)
1f: SCOP_d4dpgg1 (G:72-221)
1g: SCOP_d4dpgh1 (H:71-221)
1h: SCOP_d4dpgb1 (B:71-221)
2a: SCOP_d4dpga2 (A:222-575)
2b: SCOP_d4dpgc2 (C:222-575)
2c: SCOP_d4dpgd2 (D:222-575)
2d: SCOP_d4dpge2 (E:222-575)
2e: SCOP_d4dpgf2 (F:222-575)
2f: SCOP_d4dpgg2 (G:222-575)
2g: SCOP_d4dpgh2 (H:222-575)
2h: SCOP_d4dpgb2 (B:222-576)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
OB-fold
(1179)
Superfamily
:
Nucleic acid-binding proteins
(590)
Family
:
automated matches
(46)
Protein domain
:
automated matches
(46)
Human (Homo sapiens) [TaxId: 9606]
(6)
1a
d4dpga1
A:71-221
1b
d4dpgc1
C:71-221
1c
d4dpgd1
D:71-221
1d
d4dpge1
E:72-221
1e
d4dpgf1
F:71-221
1f
d4dpgg1
G:72-221
1g
d4dpgh1
H:71-221
1h
d4dpgb1
B:71-221
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Class II aaRS and biotin synthetases
(165)
Superfamily
:
Class II aaRS and biotin synthetases
(165)
Family
:
automated matches
(17)
Protein domain
:
automated matches
(17)
Human (Homo sapiens) [TaxId: 9606]
(4)
2a
d4dpga2
A:222-575
2b
d4dpgc2
C:222-575
2c
d4dpgd2
D:222-575
2d
d4dpge2
E:222-575
2e
d4dpgf2
F:222-575
2f
d4dpgg2
G:222-575
2g
d4dpgh2
H:222-575
2h
d4dpgb2
B:222-576
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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 C
Chain D
Chain E
Chain F
Chain G
Chain H
Chain I
Chain J
Chain K
Chain L
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...
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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:
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Show PDB file:
Asym.Unit (1.4 MB)
Header - Asym.Unit
Biol.Unit 1 (350 KB)
Header - Biol.Unit 1
Biol.Unit 2 (350 KB)
Header - Biol.Unit 2
Biol.Unit 3 (352 KB)
Header - Biol.Unit 3
Biol.Unit 4 (352 KB)
Header - Biol.Unit 4
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