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2XQR
Asym. Unit
Info
Asym.Unit (1.3 MB)
Biol.Unit 1 (237 KB)
Biol.Unit 2 (237 KB)
Biol.Unit 3 (237 KB)
Biol.Unit 4 (235 KB)
Biol.Unit 5 (237 KB)
Biol.Unit 6 (237 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF PLANT CELL WALL INVERTASE IN COMPLEX WITH A SPECIFIC PROTEIN INHIBITOR
Authors
:
M. Hothorn, W. Van Den Ende, W. Lammens, V. Rybin, K. Scheffzek
Date
:
07 Sep 10 (Deposition) - 06 Oct 10 (Release) - 15 Jun 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.58
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Biol. Unit 4: G,H (1x)
Biol. Unit 5: I,J (1x)
Biol. Unit 6: K,L (1x)
Keywords
:
Hydrolase-Inhibitor Complex, Apoplast, Cell Wall, Hydrolase, Protein Inhibitor, Sugar Metabolism, Glycosidase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Hothorn, W. Van Den Ende, W. Lammens, V. Rybin, K. Scheffzek
Structural Insights Into The Ph-Controlled Targeting Of Plant Cell-Wall Invertase By A Specific Inhibitor Protein.
Proc. Natl. Acad. Sci. Usa V. 107 17427 2010
[
close entry info
]
Hetero Components
(6, 73)
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)
1f: BETA-D-MANNOSE (BMAf)
1g: BETA-D-MANNOSE (BMAg)
1h: BETA-D-MANNOSE (BMAh)
1i: BETA-D-MANNOSE (BMAi)
1j: BETA-D-MANNOSE (BMAj)
1k: BETA-D-MANNOSE (BMAk)
1l: BETA-D-MANNOSE (BMAl)
2a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
2b: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEb)
2c: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEc)
2d: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEd)
2e: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEe)
2f: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEf)
3a: FRUCTOSE (FRUa)
3b: FRUCTOSE (FRUb)
3c: FRUCTOSE (FRUc)
3d: FRUCTOSE (FRUd)
3e: FRUCTOSE (FRUe)
3f: FRUCTOSE (FRUf)
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)
4j: ALPHA-D-MANNOSE (MANj)
4k: ALPHA-D-MANNOSE (MANk)
4l: ALPHA-D-MANNOSE (MANl)
5a: N-ACETYL-D-GLUCOSAMINE (NAGa)
5aa: N-ACETYL-D-GLUCOSAMINE (NAGaa)
5ab: N-ACETYL-D-GLUCOSAMINE (NAGab)
5ac: N-ACETYL-D-GLUCOSAMINE (NAGac)
5ad: N-ACETYL-D-GLUCOSAMINE (NAGad)
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)
5z: N-ACETYL-D-GLUCOSAMINE (NAGz)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
12
Ligand/Ion
BETA-D-MANNOSE
2
EPE
6
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3
FRU
6
Ligand/Ion
FRUCTOSE
4
MAN
12
Ligand/Ion
ALPHA-D-MANNOSE
5
NAG
30
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
6
SO4
7
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(37, 37)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:22 , ASP A:23 , GLN A:39 , TRP A:47 , TRP A:82 , SER A:83 , ARG A:148 , ASP A:149 , GLU A:203 , TYR A:279 , ASP B:96 , LYS B:98
BINDING SITE FOR RESIDUE FRU A1000
02
AC2
SOFTWARE
ASN A:143 , ALA A:144 , SER A:145 , NAG A:2000
BINDING SITE FOR RESIDUE SO4 A2002
03
AC3
SOFTWARE
ASN A:116 , SER A:118
BINDING SITE FOR RESIDUE NAG A3000
04
AC4
SOFTWARE
ASN B:48 , ALA B:51 , VAL B:52 , ALA B:74 , LYS B:78 , LEU B:81 , VAL G:51
BINDING SITE FOR RESIDUE EPE B1000
05
AC5
SOFTWARE
ASN B:2
BINDING SITE FOR RESIDUE SO4 B1001
06
AC6
SOFTWARE
ASN C:22 , ASP C:23 , GLN C:39 , TRP C:47 , TRP C:82 , SER C:83 , ARG C:148 , ASP C:149 , GLU C:203 , TYR C:279 , TRP C:297 , ASP D:96 , LYS D:98
BINDING SITE FOR RESIDUE FRU C1000
07
AC7
SOFTWARE
ASN C:143 , ALA C:144 , SER C:145 , NAG C:2000
BINDING SITE FOR RESIDUE SO4 C2002
08
AC8
SOFTWARE
ASN C:116 , SER C:118 , ASP C:119
BINDING SITE FOR RESIDUE NAG C3000
09
AC9
SOFTWARE
ASN D:48 , ALA D:51 , VAL D:52 , ALA D:74 , LYS D:78 , LEU D:81 , HOH D:4027 , VAL E:51
BINDING SITE FOR RESIDUE EPE D1000
10
BC1
SOFTWARE
ASN E:22 , ASP E:23 , GLN E:39 , TRP E:47 , TRP E:82 , SER E:83 , ARG E:148 , ASP E:149 , GLU E:203 , TYR E:279 , TRP E:297 , ASP F:96 , LYS F:98
BINDING SITE FOR RESIDUE FRU E1000
11
BC2
SOFTWARE
ASN E:143 , ALA E:144 , SER E:145 , NAG E:2000
BINDING SITE FOR RESIDUE SO4 E2002
12
BC3
SOFTWARE
ASN E:116
BINDING SITE FOR RESIDUE NAG E3000
13
BC4
SOFTWARE
VAL C:51 , ASN F:48 , ALA F:51 , VAL F:52 , ALA F:74 , LYS F:78 , LEU F:81
BINDING SITE FOR RESIDUE EPE F1000
14
BC5
SOFTWARE
ASN G:22 , ASP G:23 , GLN G:39 , TRP G:47 , TRP G:82 , SER G:83 , ARG G:148 , ASP G:149 , GLU G:203 , TYR G:279 , ASP H:96 , LYS H:98
BINDING SITE FOR RESIDUE FRU G1000
15
BC6
SOFTWARE
ASN G:143 , ALA G:144 , SER G:145 , NAG G:2000 , HOH G:4100
BINDING SITE FOR RESIDUE SO4 G2002
16
BC7
SOFTWARE
ASN G:116 , SER G:118
BINDING SITE FOR RESIDUE NAG G3000
17
BC8
SOFTWARE
ASN H:48 , ALA H:51 , VAL H:52 , ALA H:74 , LYS H:78 , LEU H:81
BINDING SITE FOR RESIDUE EPE H1000
18
BC9
SOFTWARE
ASN I:22 , ASP I:23 , GLN I:39 , TRP I:47 , TRP I:82 , SER I:83 , ARG I:148 , ASP I:149 , GLU I:203 , ASP J:96 , LYS J:98
BINDING SITE FOR RESIDUE FRU I1000
19
CC1
SOFTWARE
ASN I:143 , ALA I:144 , SER I:145 , NAG I:2000
BINDING SITE FOR RESIDUE SO4 I2002
20
CC2
SOFTWARE
ASN I:116 , SER I:118 , ASP I:119
BINDING SITE FOR RESIDUE NAG I3000
21
CC3
SOFTWARE
ASN J:48 , ALA J:51 , VAL J:52 , ALA J:74 , LYS J:78 , LEU J:81 , HOH J:4030 , VAL K:51 , PHE K:71
BINDING SITE FOR RESIDUE EPE J1000
22
CC4
SOFTWARE
ASN K:22 , ASP K:23 , GLN K:39 , TRP K:47 , TRP K:82 , SER K:83 , ARG K:148 , ASP K:149 , GLU K:203 , TYR K:279 , ASP L:96 , LYS L:98
BINDING SITE FOR RESIDUE FRU K1000
23
CC5
SOFTWARE
ASN K:143 , ALA K:144 , SER K:145 , NAG K:2000 , HOH K:4097 , HOH K:4098
BINDING SITE FOR RESIDUE SO4 K2002
24
CC6
SOFTWARE
ASN K:116 , SER K:118 , ASP K:119 , HOH K:4099
BINDING SITE FOR RESIDUE NAG K3000
25
CC7
SOFTWARE
VAL I:51 , ASN L:48 , ALA L:51 , VAL L:52 , ALA L:74 , LYS L:78 , LEU L:81
BINDING SITE FOR RESIDUE EPE L1000
26
CC8
SOFTWARE
GLY A:141 , ASN A:143 , LYS A:168 , HIS A:170 , SO4 A:2002
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 143 RESIDUES 2000 TO 2001
27
CC9
SOFTWARE
LYS A:242 , LYS A:277 , ASN A:299 , GLU A:300 , SER A:301 , SER A:400 , LYS A:401 , ASP A:461 , THR A:463 , HOH A:4104 , HOH A:4120 , HOH A:4121 , HOH A:4122 , VAL B:105 , HOH B:4023
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 299 RESIDUES 1001 TO 1006
28
DC1
SOFTWARE
ASN C:143 , LYS C:168 , ILE C:169 , HIS C:170 , SO4 C:2002 , HOH C:4040
BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 143 RESIDUES 2000 TO 2001
29
DC2
SOFTWARE
LYS C:242 , LYS C:277 , TRP C:297 , ASN C:299 , GLU C:300 , SER C:301 , GLN C:396 , SER C:400 , LYS C:401 , ASP C:461 , THR C:463 , HOH C:4071 , HOH C:4073 , HOH C:4117 , HOH C:4118 , VAL D:105 , GLU I:187
BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 299 RESIDUES 1001 TO 1006
30
DC3
SOFTWARE
ASN E:143 , LYS E:168 , ILE E:169 , HIS E:170 , SO4 E:2002
BINDING SITE FOR CHAIN E OF SUGAR BOUND TO ASN E 143 RESIDUES 2000 TO 2001
31
DC4
SOFTWARE
LYS E:242 , LYS E:277 , ASN E:299 , GLU E:300 , SER E:400 , LYS E:401 , ASP E:461 , THR E:463 , HOH E:4048 , HOH E:4106 , HOH E:4107 , HOH E:4109 , HOH E:4110 , VAL F:105 , HOH F:4015
BINDING SITE FOR CHAIN E OF SUGAR BOUND TO ASN E 299 RESIDUES 1001 TO 1006
32
DC5
SOFTWARE
ASN G:143 , LYS G:168 , ILE G:169 , HIS G:170 , SO4 G:2002
BINDING SITE FOR CHAIN G OF SUGAR BOUND TO ASN G 143 RESIDUES 2000 TO 2001
33
DC6
SOFTWARE
LYS G:242 , LYS G:277 , TRP G:297 , ASN G:299 , GLU G:300 , GLN G:396 , SER G:400 , LYS G:401 , ASP G:461 , THR G:463 , HOH G:4068 , HOH G:4083 , VAL H:105 , HOH H:4015
BINDING SITE FOR CHAIN G OF SUGAR BOUND TO ASN G 299 RESIDUES 1001 TO 1006
34
DC7
SOFTWARE
ASN I:143 , LYS I:168 , ILE I:169 , HIS I:170 , SO4 I:2002
BINDING SITE FOR CHAIN I OF SUGAR BOUND TO ASN I 143 RESIDUES 2000 TO 2001
35
DC8
SOFTWARE
LYS I:242 , LYS I:277 , TRP I:297 , ASN I:299 , GLU I:300 , SER I:301 , SER I:400 , LYS I:401 , ASP I:461 , THR I:463 , HOH I:4105 , HOH I:4106 , HOH I:4107 , VAL J:105
BINDING SITE FOR CHAIN I OF SUGAR BOUND TO ASN I 299 RESIDUES 1001 TO 1006
36
DC9
SOFTWARE
ASN K:143 , LYS K:168 , HIS K:170 , SO4 K:2002
BINDING SITE FOR CHAIN K OF SUGAR BOUND TO ASN K 143 RESIDUES 2000 TO 2001
37
EC1
SOFTWARE
LYS K:242 , LYS K:277 , TYR K:279 , TRP K:297 , ASN K:299 , GLU K:300 , LEU K:397 , SER K:400 , LYS K:401 , ASP K:461 , THR K:463 , HOH K:4095 , HOH K:4096 , VAL L:105
BINDING SITE FOR CHAIN K OF SUGAR BOUND TO ASN K 299 RESIDUES 1001 TO 1006
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(1, 6)
Info
All PROSITE Patterns/Profiles
1: GLYCOSYL_HYDROL_F32 (A:13-26,C:13-26,E:13-26,G:13-26,I:...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GLYCOSYL_HYDROL_F32
PS00609
Glycosyl hydrolases family 32 active site.
INV1_ARATH
56-69
6
A:13-26
C:13-26
E:13-26
G:13-26
I:13-26
K:13-26
[
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
(1, 6)
Info
All SCOP Domains
1a: SCOP_d2xqrb_ (B:)
1b: SCOP_d2xqrl_ (L:)
1c: SCOP_d2xqrd_ (D:)
1d: SCOP_d2xqrf_ (F:)
1e: SCOP_d2xqrh_ (H:)
1f: SCOP_d2xqrj_ (J:)
View:
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(
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Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Bromodomain-like
(339)
Superfamily
:
Plant invertase/pectin methylesterase inhibitor
(12)
Family
:
Plant invertase/pectin methylesterase inhibitor
(11)
Protein domain
:
automated matches
(6)
Tobacco (Nicotiana tabacum) [TaxId: 4097]
(6)
1a
d2xqrb_
B:
1b
d2xqrl_
L:
1c
d2xqrd_
D:
1d
d2xqrf_
F:
1e
d2xqrh_
H:
1f
d2xqrj_
J:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(3, 18)
Info
all PFAM domains
1a: PFAM_Glyco_hydro_32N_2xqrK01 (K:13-335)
1b: PFAM_Glyco_hydro_32N_2xqrK02 (K:13-335)
1c: PFAM_Glyco_hydro_32N_2xqrK03 (K:13-335)
1d: PFAM_Glyco_hydro_32N_2xqrK04 (K:13-335)
1e: PFAM_Glyco_hydro_32N_2xqrK05 (K:13-335)
1f: PFAM_Glyco_hydro_32N_2xqrK06 (K:13-335)
2a: PFAM_Glyco_hydro_32C_2xqrK07 (K:386-495)
2b: PFAM_Glyco_hydro_32C_2xqrK08 (K:386-495)
2c: PFAM_Glyco_hydro_32C_2xqrK09 (K:386-495)
2d: PFAM_Glyco_hydro_32C_2xqrK10 (K:386-495)
2e: PFAM_Glyco_hydro_32C_2xqrK11 (K:386-495)
2f: PFAM_Glyco_hydro_32C_2xqrK12 (K:386-495)
3a: PFAM_PMEI_2xqrL01 (L:2-142)
3b: PFAM_PMEI_2xqrL02 (L:2-142)
3c: PFAM_PMEI_2xqrL03 (L:2-142)
3d: PFAM_PMEI_2xqrL04 (L:2-142)
3e: PFAM_PMEI_2xqrL05 (L:2-142)
3f: PFAM_PMEI_2xqrL06 (L:2-142)
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Clans
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Families
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Organisms
(
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(
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Clan
:
B_Fructosidase
(34)
Family
:
Glyco_hydro_32N
(13)
Arabidopsis thaliana (Mouse-ear cress)
(4)
1a
Glyco_hydro_32N-2xqrK01
K:13-335
1b
Glyco_hydro_32N-2xqrK02
K:13-335
1c
Glyco_hydro_32N-2xqrK03
K:13-335
1d
Glyco_hydro_32N-2xqrK04
K:13-335
1e
Glyco_hydro_32N-2xqrK05
K:13-335
1f
Glyco_hydro_32N-2xqrK06
K:13-335
Clan
:
no clan defined [family: Glyco_hydro_32C]
(13)
Family
:
Glyco_hydro_32C
(13)
Arabidopsis thaliana (Mouse-ear cress)
(4)
2a
Glyco_hydro_32C-2xqrK07
K:386-495
2b
Glyco_hydro_32C-2xqrK08
K:386-495
2c
Glyco_hydro_32C-2xqrK09
K:386-495
2d
Glyco_hydro_32C-2xqrK10
K:386-495
2e
Glyco_hydro_32C-2xqrK11
K:386-495
2f
Glyco_hydro_32C-2xqrK12
K:386-495
Clan
:
no clan defined [family: PMEI]
(6)
Family
:
PMEI
(6)
Nicotiana tabacum (Common tobacco)
(3)
3a
PMEI-2xqrL01
L:2-142
3b
PMEI-2xqrL02
L:2-142
3c
PMEI-2xqrL03
L:2-142
3d
PMEI-2xqrL04
L:2-142
3e
PMEI-2xqrL05
L:2-142
3f
PMEI-2xqrL06
L:2-142
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
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Protein
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Protein & NOT Site
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Chain D
Chain E
Chain F
Chain G
Chain H
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Chain J
Chain K
Chain L
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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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View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
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