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1TG7
Asym. Unit
Info
Asym.Unit (195 KB)
Biol.Unit 1 (186 KB)
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(1)
Title
:
NATIVE STRUCTURE OF BETA-GALACTOSIDASE FROM PENICILLIUM SP.
Authors
:
A. L. Rojas, R. A. P. Nagem, K. N. Neustroev, M. Arand, M. Adamska, E. V. En A. A. Kulminskaya, R. C. Garratt, A. M. Golubev, I. Polikarpov
Date
:
28 May 04 (Deposition) - 02 Nov 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Tim Barrel Domain, Glycoside Hydrolase, Family Gh35, Glycoprotein, Penicillium, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. L. Rojas, R. A. P. Nagem, K. N. Neustroev, M. Arand, M. Adamska, E. V. Eneyskaya, A. A. Kulminskaya, R. C. Garratt, A. M. Golubev, I. Polikarpov
Crystal Structures Of Beta-Galactosidase From Penicillium Sp. And Its Complex With Galactose
J. Mol. Biol. V. 343 1281 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(6, 44)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
1c: BETA-D-MANNOSE (BMAc)
1d: BETA-D-MANNOSE (BMAd)
1e: BETA-D-MANNOSE (BMAe)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
3a: ALPHA-D-MANNOSE (MANa)
3b: ALPHA-D-MANNOSE (MANb)
3c: ALPHA-D-MANNOSE (MANc)
3d: ALPHA-D-MANNOSE (MANd)
3e: ALPHA-D-MANNOSE (MANe)
3f: ALPHA-D-MANNOSE (MANf)
3g: ALPHA-D-MANNOSE (MANg)
3h: ALPHA-D-MANNOSE (MANh)
3i: ALPHA-D-MANNOSE (MANi)
3j: ALPHA-D-MANNOSE (MANj)
3k: ALPHA-D-MANNOSE (MANk)
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)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
4c: SODIUM ION (NAc)
6a: PHOSPHATE ION (PO4a)
6b: PHOSPHATE ION (PO4b)
6c: PHOSPHATE ION (PO4c)
6d: PHOSPHATE ION (PO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
5
Ligand/Ion
BETA-D-MANNOSE
2
EDO
9
Ligand/Ion
1,2-ETHANEDIOL
3
MAN
11
Ligand/Ion
ALPHA-D-MANNOSE
4
NA
3
Ligand/Ion
SODIUM ION
5
NAG
12
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
6
PO4
4
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(44, 44)
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: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:364 , SER A:370 , SER A:372 , ASN A:374 , TYR A:912 , THR A:986 , THR A:987 , NAG A:1992 , HOH A:9283 , HOH A:9419 , HOH A:9536 , HOH A:9609
BINDING SITE FOR RESIDUE NAG A 1991
02
AC2
SOFTWARE
PHE A:313 , ALA A:314 , ARG A:377 , NAG A:1991 , BMA A:1993 , HOH A:8164 , HOH A:8258 , HOH A:9543 , HOH A:9968
BINDING SITE FOR RESIDUE NAG A 1992
03
AC3
SOFTWARE
NAG A:1992 , HOH A:8311
BINDING SITE FOR RESIDUE BMA A 1993
04
AC4
SOFTWARE
THR A:408 , ASN A:456 , HOH A:9836 , HOH A:9945
BINDING SITE FOR RESIDUE NAG A 2001
05
AC5
SOFTWARE
TYR A:606 , ASN A:625 , THR A:987 , NAG A:3002 , HOH A:8082 , HOH A:8251 , HOH A:9256 , HOH A:9476 , HOH A:9489 , HOH A:9700
BINDING SITE FOR RESIDUE NAG A 3001
06
AC6
SOFTWARE
THR A:376 , GLU A:378 , ASN A:575 , NAG A:3001 , BMA A:3003 , MAN A:3006 , HOH A:8251 , HOH A:9351 , HOH A:9672 , HOH A:9837
BINDING SITE FOR RESIDUE NAG A 3002
07
AC7
SOFTWARE
GLU A:378 , NAG A:3002 , BMA A:3004 , MAN A:3005 , HOH A:8449 , HOH A:9718 , HOH A:9739
BINDING SITE FOR RESIDUE BMA A 3003
08
AC8
SOFTWARE
BMA A:3003 , HOH A:9718
BINDING SITE FOR RESIDUE BMA A 3004
09
AC9
SOFTWARE
GLU A:378 , ASN A:571 , BMA A:3003 , MAN A:3006 , MAN A:3007 , HOH A:8270 , HOH A:9500 , HOH A:9900 , HOH A:9976
BINDING SITE FOR RESIDUE MAN A 3005
10
BC1
SOFTWARE
ASN A:571 , NAG A:3002 , MAN A:3005 , MAN A:3009 , HOH A:8301 , HOH A:9571
BINDING SITE FOR RESIDUE MAN A 3006
11
BC2
SOFTWARE
HIS A:322 , GLU A:323 , ARG A:326 , MAN A:3005 , MAN A:3008 , HOH A:8386 , HOH A:9475 , HOH A:9514 , HOH A:9739
BINDING SITE FOR RESIDUE MAN A 3007
12
BC3
SOFTWARE
SER A:469 , PRO A:512 , MAN A:3007 , HOH A:8100 , HOH A:8415 , HOH A:8433 , HOH A:9845
BINDING SITE FOR RESIDUE MAN A 3008
13
BC4
SOFTWARE
THR A:553 , ASP A:569 , ASN A:571 , MAN A:3006 , HOH A:8027 , HOH A:9897
BINDING SITE FOR RESIDUE MAN A 3009
14
BC5
SOFTWARE
ARG A:154 , TYR A:705 , ASN A:707 , HOH A:8036 , HOH A:9297 , HOH A:9598 , HOH A:9963
BINDING SITE FOR RESIDUE NAG A 4001
15
BC6
SOFTWARE
ASN A:691 , HIS A:736 , ASN A:763 , ASN A:793 , NAG A:5002 , HOH A:8193 , HOH A:8357 , HOH A:8384
BINDING SITE FOR RESIDUE NAG A 5001
16
BC7
SOFTWARE
ASN A:793 , NAG A:5001 , HOH A:8193
BINDING SITE FOR RESIDUE NAG A 5002
17
BC8
SOFTWARE
GLN A:749 , ASN A:778 , ASN A:780 , GLN A:824 , NAG A:6002 , HOH A:8024 , HOH A:8057 , HOH A:8269 , HOH A:8303 , HOH A:8336 , HOH A:9683
BINDING SITE FOR RESIDUE NAG A 6001
18
BC9
SOFTWARE
GLN A:714 , NAG A:6001 , BMA A:6003 , MAN A:6004 , HOH A:8024
BINDING SITE FOR RESIDUE NAG A 6002
19
CC1
SOFTWARE
GLY A:741 , THR A:787 , LEU A:788 , NAG A:6002 , MAN A:6004 , HOH A:8328
BINDING SITE FOR RESIDUE BMA A 6003
20
CC2
SOFTWARE
THR A:787 , GLN A:789 , NAG A:6002 , BMA A:6003 , MAN A:6005
BINDING SITE FOR RESIDUE MAN A 6004
21
CC3
SOFTWARE
ALA A:710 , HIS A:711 , SER A:712 , MAN A:6004 , HOH A:9775 , HOH A:9910
BINDING SITE FOR RESIDUE MAN A 6005
22
CC4
SOFTWARE
ASN A:917 , THR A:919 , SER A:920 , TYR A:939 , ASN A:941 , ILE A:943 , GLY A:944 , PRO A:945 , GLN A:946 , THR A:947 , NAG A:7002 , NA A:9001 , NA A:9003 , HOH A:9626
BINDING SITE FOR RESIDUE NAG A 7001
23
CC5
SOFTWARE
GLY A:309 , SER A:920 , PRO A:922 , ILE A:943 , NAG A:7001 , BMA A:7003 , HOH A:8032 , HOH A:8136 , HOH A:8172 , HOH A:9276 , HOH A:9332 , HOH A:9818
BINDING SITE FOR RESIDUE NAG A 7002
24
CC6
SOFTWARE
THR A:773 , SER A:774 , ILE A:775 , NAG A:7002 , MAN A:7004 , MAN A:7005 , HOH A:9276 , HOH A:9389 , HOH A:9765
BINDING SITE FOR RESIDUE BMA A 7003
25
CC7
SOFTWARE
BMA A:7003 , HOH A:8085 , HOH A:8474 , EDO A:9222 , HOH A:9294 , HOH A:9628 , HOH A:9993
BINDING SITE FOR RESIDUE MAN A 7004
26
CC8
SOFTWARE
THR A:773 , ASN A:776 , BMA A:7003 , MAN A:7006 , MAN A:7007 , HOH A:8159 , HOH A:9389 , HOH A:9730 , HOH A:9814 , HOH A:9883
BINDING SITE FOR RESIDUE MAN A 7005
27
CC9
SOFTWARE
GLY A:247 , THR A:248 , GLY A:249 , MAN A:7005 , HOH A:8041 , HOH A:8149 , HOH A:9643 , HOH A:9724
BINDING SITE FOR RESIDUE MAN A 7006
28
DC1
SOFTWARE
ASN A:776 , MAN A:7005 , HOH A:8103 , HOH A:8326 , HOH A:8336 , HOH A:9398
BINDING SITE FOR RESIDUE MAN A 7007
29
DC2
SOFTWARE
ASN A:917 , THR A:919 , NAG A:7001 , HOH A:8170
BINDING SITE FOR RESIDUE NA A 9001
30
DC3
SOFTWARE
LYS A:499 , ALA A:597 , HOH A:8052 , HOH A:9520 , HOH A:9877
BINDING SITE FOR RESIDUE NA A 9002
31
DC4
SOFTWARE
PRO A:945 , NAG A:7001 , HOH A:9645 , HOH A:9852
BINDING SITE FOR RESIDUE NA A 9003
32
DC5
SOFTWARE
HIS A:356 , PRO A:357 , GLY A:358 , ASP A:806 , GLU A:807 , HOH A:8312 , HOH A:9313 , HOH A:9638 , HOH A:9855 , HOH A:9901
BINDING SITE FOR RESIDUE PO4 A 9111
33
DC6
SOFTWARE
TRP A:770 , ASN A:779 , ASN A:780 , ALA A:781 , HOH A:8321 , HOH A:9409 , HOH A:9533
BINDING SITE FOR RESIDUE PO4 A 9112
34
DC7
SOFTWARE
THR A:699 , SER A:700 , ASP A:702 , HIS A:703 , TYR A:724 , HOH A:8341 , HOH A:8435 , HOH A:8466 , HOH A:9621
BINDING SITE FOR RESIDUE PO4 A 9113
35
DC8
SOFTWARE
SER A:674 , LYS A:676 , GLU A:982 , HOH A:8361 , HOH A:9329 , HOH A:9434
BINDING SITE FOR RESIDUE PO4 A 9114
36
DC9
SOFTWARE
LEU A:60 , MET A:61 , ALA A:390 , LYS A:391 , SER A:393 , PRO A:394 , LEU A:397 , HOH A:8225 , HOH A:9442 , HOH A:9517
BINDING SITE FOR RESIDUE EDO A 9221
37
EC1
SOFTWARE
TRP A:308 , SER A:774 , ILE A:775 , MAN A:7004 , HOH A:9788
BINDING SITE FOR RESIDUE EDO A 9222
38
EC2
SOFTWARE
ASN A:575 , THR A:627 , HOH A:8275 , HOH A:9672
BINDING SITE FOR RESIDUE EDO A 9223
39
EC3
SOFTWARE
TYR A:912 , ASN A:914 , SER A:948 , ILE A:984 , HOH A:8286 , HOH A:9543 , HOH A:9741
BINDING SITE FOR RESIDUE EDO A 9224
40
EC4
SOFTWARE
HIS A:286 , GLU A:287 , PRO A:401 , HOH A:9371 , HOH A:9466 , HOH A:9647 , HOH A:9697
BINDING SITE FOR RESIDUE EDO A 9225
41
EC5
SOFTWARE
ILE A:762 , ASN A:763 , THR A:765 , PRO A:786 , TYR A:794 , HOH A:8183 , HOH A:9637
BINDING SITE FOR RESIDUE EDO A 9226
42
EC6
SOFTWARE
THR A:280 , THR A:284 , ASP A:403 , LEU A:404 , HOH A:8206 , HOH A:9693
BINDING SITE FOR RESIDUE EDO A 9227
43
EC7
SOFTWARE
ASN A:140 , GLU A:142 , TYR A:261 , PHE A:265 , PHE A:305 , TYR A:343 , TYR A:365 , HOH A:8169 , EDO A:9229
BINDING SITE FOR RESIDUE EDO A 9228
44
EC8
SOFTWARE
TYR A:96 , ILE A:139 , ASN A:140 , ALA A:141 , ASN A:199 , GLU A:200 , GLU A:299 , EDO A:9228
BINDING SITE FOR RESIDUE EDO A 9229
[
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
(1, 1)
Info
All PROSITE Patterns/Profiles
1: GLYCOSYL_HYDROL_F35 (A:189-201)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GLYCOSYL_HYDROL_F35
PS01182
Glycosyl hydrolases family 35 putative active site.
BGALA_PENSQ
189-201
1
A:189-201
[
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.
SCOP Domains
(4, 5)
Info
All SCOP Domains
1a: SCOP_d1tg7a1 (A:570-666)
2a: SCOP_d1tg7a2 (A:667-848)
2b: SCOP_d1tg7a3 (A:849-1011)
3a: SCOP_d1tg7a4 (A:395-569)
4a: SCOP_d1tg7a5 (A:41-394)
View:
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Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Beta-galactosidase LacA, domain 3
(7)
Superfamily
:
Beta-galactosidase LacA, domain 3
(7)
Family
:
Beta-galactosidase LacA, domain 3
(2)
Protein domain
:
Beta-galactosidase LacA, domain 3
(2)
Penicillium sp. [TaxId: 5081]
(2)
1a
d1tg7a1
A:570-666
Fold
:
Galactose-binding domain-like
(314)
Superfamily
:
Galactose-binding domain-like
(314)
Family
:
Beta-galactosidase LacA, domains 4 and 5
(2)
Protein domain
:
Beta-galactosidase LacA, domains 4 and 5
(2)
Penicillium sp. [TaxId: 5081]
(2)
2a
d1tg7a2
A:667-848
2b
d1tg7a3
A:849-1011
Fold
:
Glycosyl hydrolase domain
(397)
Superfamily
:
Glycosyl hydrolase domain
(397)
Family
:
Beta-galactosidase LacA, domain 2
(2)
Protein domain
:
Beta-galactosidase LacA, domain 2
(2)
Penicillium sp. [TaxId: 5081]
(2)
3a
d1tg7a4
A:395-569
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
(Trans)glycosidases
(1191)
Family
:
Glycosyl hydrolases family 35 catalytic domain
(2)
Protein domain
:
Beta-galactosidase LacA, N-terminal domain
(2)
Penicillium sp. [TaxId: 5081]
(2)
4a
d1tg7a5
A:41-394
[
close SCOP info
]
CATH Domains
(4, 5)
Info
all CATH domains
1a: CATH_1tg7A01 (A:41-395)
2a: CATH_1tg7A02 (A:396-576)
3a: CATH_1tg7A03 (A:577-665)
4a: CATH_1tg7A05 (A:686-861)
4b: CATH_1tg7A04 (A:666-685,A:862-1011)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Glycosidases
(843)
Penicillium sp.. Organism_taxid: 5081
(2)
1a
1tg7A01
A:41-395
Class
:
Mainly Beta
(13760)
Architecture
:
3-layer Sandwich
(102)
Topology
:
beta-galactosidase, domain 2
(2)
Homologous Superfamily
:
beta-galactosidase, domain 2
(2)
Penicillium sp.. Organism_taxid: 5081
(2)
2a
1tg7A02
A:396-576
Architecture
:
Sandwich
(5577)
Topology
:
beta-galactosidase, domain 3
(2)
Homologous Superfamily
:
beta-galactosidase, domain 3
(2)
Penicillium sp.. Organism_taxid: 5081
(2)
3a
1tg7A03
A:577-665
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
Galactose-binding domain-like
(195)
Penicillium sp.. Organism_taxid: 5081
(2)
4a
1tg7A05
A:686-861
4b
1tg7A04
A:666-685,A:862-1011
[
close CATH info
]
Pfam Domains
(4, 5)
Info
all PFAM domains
1a: PFAM_BetaGal_dom4_5_1tg7A01 (A:862-975)
1b: PFAM_BetaGal_dom4_5_1tg7A02 (A:862-975)
2a: PFAM_Glyco_hydro_35_1tg7A03 (A:52-390)
3a: PFAM_BetaGal_dom2_1tg7A04 (A:396-576)
4a: PFAM_BetaGal_dom3_1tg7A05 (A:577-661)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
GBD
(153)
Family
:
BetaGal_dom4_5
(2)
Penicillium sp
(2)
1a
BetaGal_dom4_5-1tg7A01
A:862-975
1b
BetaGal_dom4_5-1tg7A02
A:862-975
Clan
:
Glyco_hydro_tim
(488)
Family
:
Glyco_hydro_35
(2)
Penicillium sp
(2)
2a
Glyco_hydro_35-1tg7A03
A:52-390
Clan
:
no clan defined [family: BetaGal_dom2]
(2)
Family
:
BetaGal_dom2
(2)
Penicillium sp
(2)
3a
BetaGal_dom2-1tg7A04
A:396-576
Clan
:
no clan defined [family: BetaGal_dom3]
(2)
Family
:
BetaGal_dom3
(2)
Penicillium sp
(2)
4a
BetaGal_dom3-1tg7A05
A:577-661
[
close Pfam info
]
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all
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Protein
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All Atoms
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Chain A
Asymmetric Unit 1
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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)
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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") .
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Asym.Unit (195 KB)
Header - Asym.Unit
Biol.Unit 1 (186 KB)
Header - Biol.Unit 1
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