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1O7D
Asym. Unit
Info
Asym.Unit (149 KB)
Biol.Unit 1 (141 KB)
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(1)
Title
:
THE STRUCTURE OF THE BOVINE LYSOSOMAL A-MANNOSIDASE SUGGESTS A NOVEL MECHANISM FOR LOW PH ACTIVATION
Authors
:
P. Heikinheimo, R. Helland, H. S. Leiros, I. Leiros, S. Karlsen, G. Evjen, R. Ravelli, G. Schoehn, R. Ruigrok, O. -K. Tollersrud, S. Mcsweeney, E. Hough
Date
:
30 Oct 02 (Deposition) - 20 Mar 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B,C,D,E (1x)
Keywords
:
Hydrolase, Glycosyl Hydrolase Family 38, A-Mannosidase, Lysosomal
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Heikinheimo, R. Helland, H. S. Leiros, I. Leiros, S. Karlsen, G. Evjen, R. Ravelli, G. Schoehn, R. Ruigrok, O. -K. Tollersrud, S. Mcsweeney, E. Hough
The Structure Of Bovine Lysosomal Alpha-Mannosidase Suggests A Novel Mechanism For Low-Ph Activation
J. Mol. Biol. V. 327 631 2003
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(7, 20)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
2a: ALPHA-D-MANNOSE (MANa)
2b: ALPHA-D-MANNOSE (MANb)
2c: ALPHA-D-MANNOSE (MANc)
2d: ALPHA-D-MANNOSE (MANd)
2e: ALPHA-D-MANNOSE (MANe)
2f: ALPHA-D-MANNOSE (MANf)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
3d: N-ACETYL-D-GLUCOSAMINE (NAGd)
3e: N-ACETYL-D-GLUCOSAMINE (NAGe)
3f: N-ACETYL-D-GLUCOSAMINE (NAGf)
3g: N-ACETYL-D-GLUCOSAMINE (NAGg)
4a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
4b: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGb)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
6a: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSa)
7a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
1
Ligand/Ion
BETA-D-MANNOSE
2
MAN
6
Ligand/Ion
ALPHA-D-MANNOSE
3
NAG
7
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
NDG
2
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
5
SO4
2
Ligand/Ion
SULFATE ION
6
TRS
1
Ligand/Ion
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
7
ZN
1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(20, 20)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:133
BINDING SITE FOR RESIDUE NAG A 1
02
AC2
SOFTWARE
ALA B:397 , LEU B:398 , NDG C:1 , BMA C:3 , SER D:834 , GLY D:835
BINDING SITE FOR RESIDUE NAG C 2
03
AC3
SOFTWARE
NAG C:2 , MAN C:13 , MAN C:16 , SER C:466
BINDING SITE FOR RESIDUE BMA C 3
04
AC4
SOFTWARE
BMA C:3 , MAN C:14 , SER C:466 , ARG C:494
BINDING SITE FOR RESIDUE MAN C 13
05
AC5
SOFTWARE
MAN C:13 , SER C:466 , GLU C:467
BINDING SITE FOR RESIDUE MAN C 14
06
AC6
SOFTWARE
BMA C:3 , MAN C:163 , MAN C:166 , ASN C:459
BINDING SITE FOR RESIDUE MAN C 16
07
AC7
SOFTWARE
MAN C:16 , SER D:834
BINDING SITE FOR RESIDUE MAN C 163
08
AC8
SOFTWARE
MAN C:16 , MAN C:167 , ASN C:459
BINDING SITE FOR RESIDUE MAN C 166
09
AC9
SOFTWARE
THR A:80 , GLN A:83 , GLU A:286 , MAN C:166 , HIS C:456 , ASP C:460
BINDING SITE FOR RESIDUE MAN C 167
10
BC1
SOFTWARE
ALA B:397 , TYR B:401 , LEU B:404 , NAG C:2 , ASN C:497 , TRP D:837 , VAL D:838 , ARG D:839
BINDING SITE FOR RESIDUE NDG C 1
11
BC2
SOFTWARE
NDG D:11 , ASN D:645 , ASN D:665 , GLN D:666 , LEU D:670 , TRP D:725
BINDING SITE FOR RESIDUE NAG D 1
12
BC3
SOFTWARE
NAG D:1 , TRP D:725
BINDING SITE FOR RESIDUE NDG D 11
13
BC4
SOFTWARE
NAG D:21 , ASN D:692
BINDING SITE FOR RESIDUE NAG D 2
14
BC5
SOFTWARE
NAG D:2 , ALA D:695
BINDING SITE FOR RESIDUE NAG D 21
15
BC6
SOFTWARE
PRO B:384 , TYR B:385 , NAG D:31 , ASN D:766
BINDING SITE FOR RESIDUE NAG D 3
16
BC7
SOFTWARE
NAG D:3
BINDING SITE FOR RESIDUE NAG D 31
17
BC8
SOFTWARE
TRS A:2 , HIS A:72 , ASP A:74 , ASP A:196 , HIS C:446
BINDING SITE FOR RESIDUE ZN A 3
18
BC9
SOFTWARE
GLY A:51 , TYR A:52 , LYS A:53 , ARG A:190
BINDING SITE FOR RESIDUE SO4 A3001
19
CC1
SOFTWARE
PRO E:910 , GLU E:911 , THR E:912
BINDING SITE FOR RESIDUE SO4 E3002
20
CC2
SOFTWARE
ZN A:3 , HIS A:72 , ASP A:74 , TRP A:77 , ASP A:196 , PHE A:198 , ARG A:220 , HIS C:446 , ASP C:447 , TYR D:660
BINDING SITE FOR RESIDUE TRS A 2
[
close Site info
]
SAPs(SNPs)/Variants
(2, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_MA2B1_BOVIN_001 (R220H, chain A, )
2: VAR_MA2B1_BOVIN_002 (F320L, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_MA2B1_BOVIN_001
*
R
221
H
MA2B1_BOVIN
---
---
A
R
220
H
2
UniProt
VAR_MA2B1_BOVIN_002
*
F
321
L
MA2B1_BOVIN
---
---
A
F
320
L
* ID not provided by source
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
(24, 27)
Info
All Exons
Exon 1.1 (A:51-53 | - | - | - | -)
Exon 1.2 (A:54-88 | - | - | - | -)
Exon 1.3 (A:88-146 | - | - | - | -)
Exon 1.4 (A:146-210 | - | - | - | -)
Exon 1.5 (A:211-255 | - | - | - | -)
Exon 1.6 (A:255-303 | - | - | - | -)
Exon 1.7 (A:304-342 | - | - | - | -)
Exon 1.8 (- | B:347-370 | - | - | -)
Exon 1.9 (- | B:370-410 | - | - | -)
Exon 1.10 (- | B:411-422 | C:431-437 | - | -)
Exon 1.11 (- | - | C:437-473 | - | -)
Exon 1.12 (- | - | C:474-509 | - | -)
Exon 1.13 (- | - | C:510-548 | - | -)
Exon 1.14 (- | - | C:549-585 (gaps) | D:603-6...)
Exon 1.15 (- | - | - | D:611-643 (gaps) | -)
Exon 1.16 (- | - | - | D:643-682 | -)
Exon 1.17 (- | - | - | D:683-722 | -)
Exon 1.18 (- | - | - | D:722-756 | -)
Exon 1.19 (- | - | - | D:756-785 | -)
Exon 1.20 (- | - | - | D:786-812 | -)
Exon 1.21 (- | - | - | D:813-875 | E:885-888)
Exon 1.22 (- | - | - | - | E:889-940)
Exon 1.23 (- | - | - | - | E:941-973)
Exon 1.24 (- | - | - | - | E:988-1007)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1
02: Boundary 1.1/1.2
03: Boundary 1.2/1.3
04: Boundary 1.3/1.4
05: Boundary 1.4/1.5
06: Boundary 1.5/1.6
07: Boundary 1.6/1.7
08: Boundary 1.7/1.8
09: Boundary 1.8/1.9
10: Boundary 1.9/1.10
11: Boundary 1.10/1.11
12: Boundary 1.11/1.12
13: Boundary 1.12/1.13
14: Boundary 1.13/1.14
15: Boundary 1.14/1.15
16: Boundary 1.15/1.16
17: Boundary 1.16/1.17
18: Boundary 1.17/1.18
19: Boundary 1.18/1.19
20: Boundary 1.19/1.20
21: Boundary 1.20/1.21
22: Boundary 1.21/1.22
23: Boundary 1.22/1.23
24: Boundary 1.23/1.24
25: Boundary 1.24/-
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
ENSBTAT00000008193
1
ENSBTAE00000066219
chr7:
11107376-11107551
176
MA2B1_BOVIN
1-54
54
1
A:51-53
-
-
-
-
3
-
-
-
-
1.2
ENSBTAT00000008193
2
ENSBTAE00000284075
chr7:
11108225-11108327
103
MA2B1_BOVIN
55-89
35
1
A:54-88
-
-
-
-
35
-
-
-
-
1.3
ENSBTAT00000008193
3
ENSBTAE00000284074
chr7:
11108505-11108678
174
MA2B1_BOVIN
89-147
59
1
A:88-146
-
-
-
-
59
-
-
-
-
1.4
ENSBTAT00000008193
4
ENSBTAE00000284070
chr7:
11109063-11109256
194
MA2B1_BOVIN
147-211
65
1
A:146-210
-
-
-
-
65
-
-
-
-
1.5
ENSBTAT00000008193
5
ENSBTAE00000284068
chr7:
11109905-11110037
133
MA2B1_BOVIN
212-256
45
1
A:211-255
-
-
-
-
45
-
-
-
-
1.6
ENSBTAT00000008193
6
ENSBTAE00000066226
chr7:
11110258-11110403
146
MA2B1_BOVIN
256-304
49
1
A:255-303
-
-
-
-
49
-
-
-
-
1.7
ENSBTAT00000008193
7
ENSBTAE00000066228
chr7:
11111194-11111310
117
MA2B1_BOVIN
305-343
39
1
A:304-342
-
-
-
-
39
-
-
-
-
1.8
ENSBTAT00000008193
8
ENSBTAE00000066229
chr7:
11114403-11114488
86
MA2B1_BOVIN
344-372
29
1
-
B:347-370
-
-
-
-
24
-
-
-
1.9
ENSBTAT00000008193
9
ENSBTAE00000066231
chr7:
11114572-11114692
121
MA2B1_BOVIN
372-412
41
1
-
B:370-410
-
-
-
-
41
-
-
-
1.10
ENSBTAT00000008193
10
ENSBTAE00000066233
chr7:
11114772-11114850
79
MA2B1_BOVIN
413-439
27
2
-
B:411-422
C:431-437
-
-
-
12
7
-
-
1.11
ENSBTAT00000008193
11
ENSBTAE00000066235
chr7:
11115025-11115134
110
MA2B1_BOVIN
439-475
37
1
-
-
C:437-473
-
-
-
-
37
-
-
1.12
ENSBTAT00000008193
12
ENSBTAE00000066239
chr7:
11115408-11115515
108
MA2B1_BOVIN
476-511
36
1
-
-
C:474-509
-
-
-
-
36
-
-
1.13
ENSBTAT00000008193
13
ENSBTAE00000066241
chr7:
11115808-11115924
117
MA2B1_BOVIN
512-550
39
1
-
-
C:510-548
-
-
-
-
39
-
-
1.14
ENSBTAT00000008193
14
ENSBTAE00000066243
chr7:
11116738-11116884
147
MA2B1_BOVIN
551-599
49
2
-
-
C:549-585 (gaps)
D:603-610
-
-
-
37
8
-
1.15
ENSBTAT00000008193
15
ENSBTAE00000066245
chr7:
11117958-11118055
98
MA2B1_BOVIN
600-632
33
1
-
-
-
D:611-643 (gaps)
-
-
-
-
33
-
1.16
ENSBTAT00000008193
16
ENSBTAE00000066248
chr7:
11118141-11118258
118
MA2B1_BOVIN
632-671
40
1
-
-
-
D:643-682
-
-
-
-
40
-
1.17
ENSBTAT00000008193
17
ENSBTAE00000066251
chr7:
11119833-11119951
119
MA2B1_BOVIN
672-711
40
1
-
-
-
D:683-722
-
-
-
-
40
-
1.18
ENSBTAT00000008193
18
ENSBTAE00000066254
chr7:
11120032-11120133
102
MA2B1_BOVIN
711-745
35
1
-
-
-
D:722-756
-
-
-
-
35
-
1.19
ENSBTAT00000008193
19
ENSBTAE00000066260
chr7:
11120306-11120393
88
MA2B1_BOVIN
745-774
30
1
-
-
-
D:756-785
-
-
-
-
30
-
1.20
ENSBTAT00000008193
20
ENSBTAE00000066263
chr7:
11120569-11120649
81
MA2B1_BOVIN
775-801
27
1
-
-
-
D:786-812
-
-
-
-
27
-
1.21
ENSBTAT00000008193
21
ENSBTAE00000066266
chr7:
11121072-11121299
228
MA2B1_BOVIN
802-877
76
2
-
-
-
D:813-875
E:885-888
-
-
-
63
4
1.22
ENSBTAT00000008193
22
ENSBTAE00000066268
chr7:
11121740-11121895
156
MA2B1_BOVIN
878-929
52
1
-
-
-
-
E:889-940
-
-
-
-
52
1.23
ENSBTAT00000008193
23
ENSBTAE00000066270
chr7:
11121987-11122089
103
MA2B1_BOVIN
930-964
35
1
-
-
-
-
E:941-973
-
-
-
-
33
1.24
ENSBTAT00000008193
24
ENSBTAE00000066272
chr7:
11122486-11122713
228
MA2B1_BOVIN
964-999
36
1
-
-
-
-
E:988-1007
-
-
-
-
20
[
close EXON info
]
SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d1o7d_1 (B:385-422,C:431-487)
2a: SCOP_d1o7d_2 (C:488-585,D:603-875,E:885-1007)
3a: SCOP_d1o7d_3 (A:51-342,B:347-384)
View:
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Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
immunoglobulin/albumin-binding domain-like
(130)
Superfamily
:
Families 57/38 glycoside transferase middle domain
(64)
Family
:
alpha-mannosidase, domain 2
(58)
Protein domain
:
Lysosomal alpha-mannosidase
(1)
Cow (Bos taurus) [TaxId: 9913]
(1)
1a
d1o7d.1
B:385-422,C:431-487
Class
:
All beta proteins
(24004)
Fold
:
Supersandwich
(271)
Superfamily
:
Galactose mutarotase-like
(205)
Family
:
alpha-mannosidase, C-terminal domain
(58)
Protein domain
:
Lysosomal alpha-mannosidase
(1)
Cow (Bos taurus) [TaxId: 9913]
(1)
2a
d1o7d.2
C:488-585,D:603-875,E:885-1007
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
7-stranded beta/alpha barrel
(137)
Superfamily
:
Glycoside hydrolase/deacetylase
(89)
Family
:
alpha-mannosidase
(58)
Protein domain
:
Lysosomal alpha-mannosidase
(1)
Cow (Bos taurus) [TaxId: 9913]
(1)
3a
d1o7d.3
A:51-342,B:347-384
[
close SCOP info
]
CATH Domains
(5, 5)
Info
all CATH domains
1a: CATH_1o7dA01 (A:63-342)
2a: CATH_1o7dC01 (C:431-491)
3a: CATH_1o7dD01 (D:603-866)
4a: CATH_1o7dE00 (E:885-1007)
5a: CATH_1o7dC02 (C:492-584)
View:
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Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
7-stranded beta/alpha barrel
(59)
Homologous Superfamily
:
Glycoside hydrolase 38, N terminal domain
(59)
Bovine (Bos taurus)
(1)
1a
1o7dA01
A:63-342
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Helix Hairpins
(718)
Homologous Superfamily
:
Helix hairpin bin
(1)
Bovine (Bos taurus)
(1)
2a
1o7dC01
C:431-491
Class
:
Mainly Beta
(13760)
Architecture
:
Distorted Sandwich
(506)
Topology
:
Beta-galactosidase; Chain A, domain 5
(250)
Homologous Superfamily
:
Golgi alpha-mannosidase II; domain 4
(58)
Bovine (Bos taurus)
(1)
3a
1o7dD01
D:603-866
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
[code=2.60.40.1360, no name defined]
(58)
Bovine (Bos taurus)
(1)
4a
1o7dE00
E:885-1007
Homologous Superfamily
:
Golgi alpha-mannosidase II
(346)
Bovine (Bos taurus)
(1)
5a
1o7dC02
C:492-584
[
close CATH info
]
Pfam Domains
(3, 7)
Info
all PFAM domains
1a: PFAM_Glyco_hydro_38_1o7dB01 (B:347-381)
1b: PFAM_Glyco_hydro_38_1o7dB02 (B:347-381)
2a: PFAM_Glyco_hydro_38C_1o7dE01 (E:885-1001)
2b: PFAM_Glyco_hydro_38C_1o7dE02 (E:885-1001)
2c: PFAM_Glyco_hydro_38C_1o7dE03 (E:885-1001)
3a: PFAM_Alpha_mann_mid_1o7dC01 (C:431-465)
3b: PFAM_Alpha_mann_mid_1o7dC02 (C:431-465)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
GH_CE
(28)
Family
:
Glyco_hydro_38
(17)
Bos taurus (Bovine)
(1)
1a
Glyco_hydro_38-1o7dB01
B:347-381
1b
Glyco_hydro_38-1o7dB02
B:347-381
Clan
:
Gal_mutarotase
(81)
Family
:
Glyco_hydro_38C
(17)
Bos taurus (Bovine)
(1)
2a
Glyco_hydro_38C-1o7dE01
E:885-1001
2b
Glyco_hydro_38C-1o7dE02
E:885-1001
2c
Glyco_hydro_38C-1o7dE03
E:885-1001
Clan
:
no clan defined [family: Alpha-mann_mid]
(17)
Family
:
Alpha-mann_mid
(17)
Bos taurus (Bovine)
(1)
3a
Alpha-mann_mid-1o7dC01
C:431-465
3b
Alpha-mann_mid-1o7dC02
C:431-465
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