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2Q9O
Asym. Unit
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Asym.Unit (440 KB)
Biol.Unit 1 (414 KB)
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(1)
Title
:
NEAR-ATOMIC RESOLUTION STRUCTURE OF A MELANOCARPUS ALBOMYCES LACCASE
Authors
:
N. Hakulinen, J. Rouvinen
Date
:
13 Jun 07 (Deposition) - 25 Mar 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.30
Chains
:
Asym. Unit : A,B,C
#
,D
#
,E
#
,G
#
,H
#
,I
#
,J
#
,K
#
,L
#
Biol. Unit 1: A,B (1x)
(
#
: chains that contain no standard or modified protein/DNA/RNA residue)
Keywords
:
Laccase, Multicopper Oxidase, Melanocarpus Albomyces, 2-Oxohistidine, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. Hakulinen, M. Andberg, J. Kallio, A. Koivula, K. Kruus, J. Rouvinen
A Near Atomic Resolution Structure Of A Melanocarpus Albomyces Laccase.
J. Struct. Biol. V. 162 29 2008
[
close entry info
]
Hetero Components
(8, 55)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
2a: COPPER (II) ION (CUa)
2b: COPPER (II) ION (CUb)
2c: COPPER (II) ION (CUc)
2d: COPPER (II) ION (CUd)
2e: COPPER (II) ION (CUe)
2f: COPPER (II) ION (CUf)
2g: COPPER (II) ION (CUg)
2h: COPPER (II) ION (CUh)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
4a: ALPHA-D-MANNOSE (MANa)
4b: ALPHA-D-MANNOSE (MANb)
4c: ALPHA-D-MANNOSE (MANc)
4d: ALPHA-D-MANNOSE (MANd)
4e: ALPHA-D-MANNOSE (MANe)
4f: ALPHA-D-MANNOSE (MANf)
4g: ALPHA-D-MANNOSE (MANg)
4h: ALPHA-D-MANNOSE (MANh)
4i: ALPHA-D-MANNOSE (MANi)
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)
5k: N-ACETYL-D-GLUCOSAMINE (NAGk)
5l: N-ACETYL-D-GLUCOSAMINE (NAGl)
5m: N-ACETYL-D-GLUCOSAMINE (NAGm)
5n: N-ACETYL-D-GLUCOSAMINE (NAGn)
5o: N-ACETYL-D-GLUCOSAMINE (NAGo)
5p: N-ACETYL-D-GLUCOSAMINE (NAGp)
5q: N-ACETYL-D-GLUCOSAMINE (NAGq)
5r: N-ACETYL-D-GLUCOSAMINE (NAGr)
5s: N-ACETYL-D-GLUCOSAMINE (NAGs)
5t: N-ACETYL-D-GLUCOSAMINE (NAGt)
5u: N-ACETYL-D-GLUCOSAMINE (NAGu)
5v: N-ACETYL-D-GLUCOSAMINE (NAGv)
5w: N-ACETYL-D-GLUCOSAMINE (NAGw)
5x: N-ACETYL-D-GLUCOSAMINE (NAGx)
5y: N-ACETYL-D-GLUCOSAMINE (NAGy)
6a: 3-(2-OXO-2H-IMIDAZOL-4-YL)-L-ALANI... (OHIa)
6b: 3-(2-OXO-2H-IMIDAZOL-4-YL)-L-ALANI... (OHIb)
7a: OXYGEN MOLECULE (OXYa)
7b: OXYGEN MOLECULE (OXYb)
8a: SULFATE ION (SO4a)
8b: SULFATE ION (SO4b)
8c: SULFATE ION (SO4c)
8d: SULFATE ION (SO4d)
8e: SULFATE ION (SO4e)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
2
Ligand/Ion
CHLORIDE ION
2
CU
8
Ligand/Ion
COPPER (II) ION
3
GOL
2
Ligand/Ion
GLYCEROL
4
MAN
9
Ligand/Ion
ALPHA-D-MANNOSE
5
NAG
25
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
6
OHI
2
Mod. Amino Acid
3-(2-OXO-2H-IMIDAZOL-4-YL)-L-ALANINE
7
OXY
2
Ligand/Ion
OXYGEN MOLECULE
8
SO4
5
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(51, 51)
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)
30: DC3 (SOFTWARE)
31: DC5 (SOFTWARE)
32: DC6 (SOFTWARE)
33: DC7 (SOFTWARE)
34: DC8 (SOFTWARE)
35: DC9 (SOFTWARE)
36: EC1 (SOFTWARE)
37: EC2 (SOFTWARE)
38: EC3 (SOFTWARE)
39: EC4 (SOFTWARE)
40: EC5 (SOFTWARE)
41: EC6 (SOFTWARE)
42: EC7 (SOFTWARE)
43: EC8 (SOFTWARE)
44: EC9 (SOFTWARE)
45: FC1 (SOFTWARE)
46: FC2 (SOFTWARE)
47: FC3 (SOFTWARE)
48: FC4 (SOFTWARE)
49: FC5 (SOFTWARE)
50: FC6 (SOFTWARE)
51: FC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:39 , ASN A:84 , HOH A:4382 , HOH A:4407 , HOH A:4559 , GLU B:78 , ARG B:126 , HOH B:4675
BINDING SITE FOR RESIDUE NAG A 1001
02
AC2
SOFTWARE
LYS A:56 , MET A:58 , THR A:87 , ASN A:88 , ASP A:181 , ASN A:550 , TYR A:552 , HOH A:4041 , HOH A:4054 , HOH A:4146 , HOH A:4190 , HOH C:17
BINDING SITE FOR RESIDUE NAG C 11
03
AC3
SOFTWARE
GLU A:55 , ALA A:179 , ASP A:181 , ASP A:182 , TYR A:552 , HOH A:4011 , HOH A:4401 , HOH C:14 , HOH C:15 , HOH C:16
BINDING SITE FOR RESIDUE NAG C 12
04
AC4
SOFTWARE
ASN A:216 , THR A:218 , HIS A:311 , GLY A:317 , GLY A:318 , HOH D:23 , HOH D:24
BINDING SITE FOR RESIDUE NAG D 21
05
AC5
SOFTWARE
HIS A:311 , ALA A:313 , GLY A:314 , GLY A:317 , HOH A:4399
BINDING SITE FOR RESIDUE NAG D 22
06
AC6
SOFTWARE
TRP A:287 , ASN A:289 , THR A:291 , HIS A:305 , ALA A:307 , GLU A:323 , THR A:325 , HOH A:4168 , HOH E:35 , HOH E:37
BINDING SITE FOR RESIDUE NAG E 31
07
AC7
SOFTWARE
TYR A:214 , TRP A:287 , HIS A:305 , GLU A:323 , HOH E:34 , HOH E:38
BINDING SITE FOR RESIDUE NAG E 32
08
AC8
SOFTWARE
HOH E:36
BINDING SITE FOR RESIDUE MAN E 33
09
AC9
SOFTWARE
PRO A:355 , ASP A:356 , THR A:358 , LEU A:359 , ASN A:376 , HOH A:4414 , HOH A:4618
BINDING SITE FOR RESIDUE NAG A 1002
10
BC1
SOFTWARE
PRO A:355 , ASP A:356
BINDING SITE FOR RESIDUE NAG A 1003
11
BC2
SOFTWARE
LYS A:386 , TYR A:391 , ASN A:396 , SER A:398 , HOH A:4310 , HOH A:4520 , HOH A:4661 , GLN B:530
BINDING SITE FOR RESIDUE NAG A 1051
12
BC3
SOFTWARE
LEU A:167 , PHE A:170 , ASN A:201 , LEU A:227 , HOH G:73 , HOH G:76
BINDING SITE FOR RESIDUE NAG G 61
13
BC4
SOFTWARE
ASP A:166 , GLY A:168 , HOH G:67 , HOH G:68 , HOH G:70 , HOH G:77
BINDING SITE FOR RESIDUE NAG G 62
14
BC5
SOFTWARE
HOH G:72 , HOH G:77
BINDING SITE FOR RESIDUE MAN G 63
15
BC6
SOFTWARE
HOH A:4140 , HOH A:4528 , HOH G:74
BINDING SITE FOR RESIDUE MAN G 64
16
BC7
SOFTWARE
ARG A:10 , HOH G:66 , HOH G:69
BINDING SITE FOR RESIDUE MAN G 65
17
BC8
SOFTWARE
ASN A:244 , TYR A:286 , HOH A:4257 , HOH A:4403 , HOH A:4438 , ARG B:281 , HOH B:4275
BINDING SITE FOR RESIDUE NAG A 1071
18
BC9
SOFTWARE
GLU A:78 , ARG A:126 , ASN B:39 , ASN B:84 , HOH B:4488 , HOH B:4671
BINDING SITE FOR RESIDUE NAG B 1001
19
CC1
SOFTWARE
LYS B:56 , THR B:87 , ASN B:88 , ASP B:181 , ASN B:550 , TYR B:552 , HOH B:4033 , HOH B:4034 , HOH B:4138 , HOH H:1014 , HOH H:1018
BINDING SITE FOR RESIDUE NAG H 1011
20
CC2
SOFTWARE
GLU B:55 , ALA B:179 , ASP B:181 , ASP B:182 , HOH B:4058 , HOH H:1015 , HOH H:1016 , HOH H:1017
BINDING SITE FOR RESIDUE NAG H 1012
21
CC3
SOFTWARE
HIS B:185 , HOH H:1016 , HOH H:1020 , HOH H:1021
BINDING SITE FOR RESIDUE MAN H 1013
22
CC4
SOFTWARE
ASN B:216 , THR B:218 , ILE B:309 , HIS B:311 , GLY B:317 , GLY B:318 , HOH I:1023 , HOH I:1024
BINDING SITE FOR RESIDUE NAG I 1021
23
CC5
SOFTWARE
HIS B:311 , ALA B:313 , GLY B:314 , HOH B:4427
BINDING SITE FOR RESIDUE NAG I 1022
24
CC6
SOFTWARE
TRP B:287 , ASN B:289 , HIS B:305 , ALA B:307 , GLU B:323 , THR B:325 , HOH B:4142 , HOH J:1034
BINDING SITE FOR RESIDUE NAG J 1031
25
CC7
SOFTWARE
TYR B:214 , TRP B:287 , HIS B:305 , GLU B:323 , HOH J:1034
BINDING SITE FOR RESIDUE NAG J 1032
26
CC8
SOFTWARE
PRO B:355 , ASP B:356 , THR B:358 , LEU B:359 , ASN B:376 , HOH K:1043
BINDING SITE FOR RESIDUE NAG K 1041
27
CC9
SOFTWARE
PRO B:355 , HOH K:1044
BINDING SITE FOR RESIDUE NAG K 1042
28
DC1
SOFTWARE
ASP A:379 , ASN A:381 , HOH A:4581 , LYS B:386 , ASN B:396 , HOH B:4229 , HOH B:4497 , HOH B:4569 , HOH B:4685
BINDING SITE FOR RESIDUE NAG B 1051
29
DC2
SOFTWARE
LEU B:167 , ASN B:201 , LEU B:227 , HOH L:1073
BINDING SITE FOR RESIDUE NAG L 1061
30
DC3
SOFTWARE
ASP B:166 , HOH L:1067 , HOH L:1068 , HOH L:1070 , HOH L:1072
BINDING SITE FOR RESIDUE NAG L 1062
31
DC5
SOFTWARE
ASP B:166 , HOH L:1071
BINDING SITE FOR RESIDUE MAN L 1064
32
DC6
SOFTWARE
ARG B:10 , HOH B:4677 , HOH L:1066 , HOH L:1069 , HOH L:1077 , HOH L:1078
BINDING SITE FOR RESIDUE MAN L 1065
33
DC7
SOFTWARE
HIS A:431 , CYS A:503 , ILE A:505 , HIS A:508 , LEU A:513
BINDING SITE FOR RESIDUE CU A 2001
34
DC8
SOFTWARE
HIS A:140 , HIS A:436 , HIS A:502
BINDING SITE FOR RESIDUE CU A 2002
35
DC9
SOFTWARE
HIS A:95 , TRP A:136 , HIS A:138 , HIS A:504
BINDING SITE FOR RESIDUE CU A 2003
36
EC1
SOFTWARE
HIS A:93 , HIS A:95 , HIS A:434 , HIS A:436
BINDING SITE FOR RESIDUE CU A 2004
37
EC2
SOFTWARE
HIS A:93 , GLY A:96 , HIS A:434 , HOH A:4107
BINDING SITE FOR RESIDUE CL A 2010
38
EC3
SOFTWARE
HIS B:431 , CYS B:503 , ILE B:505 , HIS B:508
BINDING SITE FOR RESIDUE CU B 2001
39
EC4
SOFTWARE
HIS B:140 , HIS B:436 , HIS B:502
BINDING SITE FOR RESIDUE CU B 2002
40
EC5
SOFTWARE
HIS B:95 , TRP B:136 , HIS B:138 , HIS B:504
BINDING SITE FOR RESIDUE CU B 2003
41
EC6
SOFTWARE
HIS B:93 , HIS B:95 , HIS B:434 , HIS B:436
BINDING SITE FOR RESIDUE CU B 2004
42
EC7
SOFTWARE
HIS B:93 , GLY B:96 , HIS B:434 , HOH B:4160
BINDING SITE FOR RESIDUE CL B 2010
43
EC8
SOFTWARE
ARG A:492 , HOH A:4612 , HOH A:4621 , ARG B:128 , ARG B:130
BINDING SITE FOR RESIDUE SO4 A 4001
44
EC9
SOFTWARE
ARG A:128 , ARG A:130 , ARG B:492
BINDING SITE FOR RESIDUE SO4 B 4002
45
FC1
SOFTWARE
ARG A:520 , ARG A:527 , HOH A:4260 , HOH A:4461 , HOH A:4513 , HOH A:4605 , HOH A:4638 , HOH A:4654 , ARG B:520 , ARG B:527
BINDING SITE FOR RESIDUE SO4 A 4003
46
FC2
SOFTWARE
PRO B:447 , ASP B:448 , ARG B:467 , HOH B:4239 , HOH B:4445
BINDING SITE FOR RESIDUE SO4 B 4004
47
FC3
SOFTWARE
PRO A:447 , ASP A:448 , ARG A:467 , HOH A:4275 , HOH A:4664
BINDING SITE FOR RESIDUE SO4 A 4005
48
FC4
SOFTWARE
HIS A:93 , HIS A:95 , HIS A:138 , HIS A:140 , HIS A:434 , HIS A:436 , HIS A:502 , HIS A:504
BINDING SITE FOR RESIDUE OXY A 4006
49
FC5
SOFTWARE
HIS B:93 , HIS B:95 , HIS B:138 , HIS B:140 , HIS B:434 , HIS B:436 , HIS B:502 , HIS B:504
BINDING SITE FOR RESIDUE OXY B 4005
50
FC6
SOFTWARE
ALA A:191 , PRO A:192 , PHE A:371 , TRP A:373 , PHE A:427 , LEU A:429 , HOH A:4082 , HOH A:4093 , HOH A:4189
BINDING SITE FOR RESIDUE GOL A 3001
51
FC7
SOFTWARE
ALA B:191 , PRO B:192 , PHE B:371 , TRP B:373 , LEU B:429 , HOH B:4059 , HOH B:4089 , HOH B:4198
BINDING SITE FOR RESIDUE GOL B 3002
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: MULTICOPPER_OXIDASE1 (A:497-517,B:497-517)
2: MULTICOPPER_OXIDASE2 (A:502-513,B:502-513)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
MULTICOPPER_OXIDASE1
PS00079
Multicopper oxidases signature 1.
LAC1_MELAO
547-567
2
A:497-517
B:497-517
2
MULTICOPPER_OXIDASE2
PS00080
Multicopper oxidases signature 2.
LAC1_MELAO
552-563
2
A:502-513
B:502-513
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
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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.
SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d2q9oa1 (A:1-162)
1b: SCOP_d2q9oa2 (A:163-343)
1c: SCOP_d2q9oa3 (A:344-559)
1d: SCOP_d2q9ob1 (B:1-162)
1e: SCOP_d2q9ob2 (B:163-343)
1f: SCOP_d2q9ob3 (B:344-559)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Cupredoxin-like
(545)
Superfamily
:
Cupredoxins
(543)
Family
:
Multidomain cupredoxins
(146)
Protein domain
:
Laccase
(13)
Fungus (Melanocarpus albomyces) [TaxId: 204285]
(8)
1a
d2q9oa1
A:1-162
1b
d2q9oa2
A:163-343
1c
d2q9oa3
A:344-559
1d
d2q9ob1
B:1-162
1e
d2q9ob2
B:163-343
1f
d2q9ob3
B:344-559
[
close SCOP info
]
CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_2q9oA01 (A:1-158)
1b: CATH_2q9oB01 (B:1-158)
1c: CATH_2q9oA02 (A:159-342)
1d: CATH_2q9oB02 (B:159-342)
1e: CATH_2q9oA03 (A:343-559)
1f: CATH_2q9oB03 (B:343-559)
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Topologies
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)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Cupredoxins - blue copper proteins
(420)
Melanocarpus albomyces. Organism_taxid: 204285. Strain: vtt d-96490.
(7)
1a
2q9oA01
A:1-158
1b
2q9oB01
B:1-158
1c
2q9oA02
A:159-342
1d
2q9oB02
B:159-342
1e
2q9oA03
A:343-559
1f
2q9oB03
B:343-559
[
close CATH info
]
Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_Cu_oxidase_2q9oB01 (B:166-315)
1b: PFAM_Cu_oxidase_2q9oB02 (B:166-315)
2a: PFAM_Cu_oxidase_2_2q9oB03 (B:359-523)
2b: PFAM_Cu_oxidase_2_2q9oB04 (B:359-523)
3a: PFAM_Cu_oxidase_3_2q9oB05 (B:41-160)
3b: PFAM_Cu_oxidase_3_2q9oB06 (B:41-160)
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Clans
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Families
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Organisms
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(
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Clan
:
CU_oxidase
(192)
Family
:
Cu-oxidase
(74)
Melanocarpus albomyces
(2)
1a
Cu-oxidase-2q9oB01
B:166-315
1b
Cu-oxidase-2q9oB02
B:166-315
Family
:
Cu-oxidase_2
(24)
Melanocarpus albomyces
(2)
2a
Cu-oxidase_2-2q9oB03
B:359-523
2b
Cu-oxidase_2-2q9oB04
B:359-523
Family
:
Cu-oxidase_3
(79)
Melanocarpus albomyces
(2)
3a
Cu-oxidase_3-2q9oB05
B:41-160
3b
Cu-oxidase_3-2q9oB06
B:41-160
[
close Pfam info
]
Atom Selection
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all
)
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Protein & NOT Variant
Protein & NOT Site
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Asymmetric Unit 1
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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)
[
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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") .
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