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2OOV
Asym. Unit
Info
Asym.Unit (741 KB)
Biol.Unit 1 (250 KB)
Biol.Unit 2 (251 KB)
Biol.Unit 3 (251 KB)
Biol.Unit 4 (730 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HANSENULA POLYMORPHA AMINE OXIDASE TO 1.7 ANGSTROMS
Authors
:
B. J. Johnson, C. M. Wilmot
Date
:
26 Jan 07 (Deposition) - 10 Apr 07 (Release) - 18 Apr 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Biol. Unit 4: A,B,C,D,E,F (1x)
Keywords
:
Protein-Derived Cofactor, Beta-Sandwich, Tpq, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. J. Johnson, J. Cohen, R. W. Welford, A. R. Pearson, K. Schulten, J. P. Klinman, C. M. Wilmot
Exploring Molecular Oxygen Pathways In Hansenula Polymorpha Copper-Containing Amine Oxidase
J. Biol. Chem. V. 282 17767 2007
[
close entry info
]
Hetero Components
(5, 44)
Info
All Hetero Components
1a: COPPER (II) ION (CUa)
1b: COPPER (II) ION (CUb)
1c: COPPER (II) ION (CUc)
1d: COPPER (II) ION (CUd)
1e: COPPER (II) ION (CUe)
1f: COPPER (II) ION (CUf)
2a: GLYCEROL (GOLa)
2aa: GLYCEROL (GOLaa)
2ab: GLYCEROL (GOLab)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
2i: GLYCEROL (GOLi)
2j: GLYCEROL (GOLj)
2k: GLYCEROL (GOLk)
2l: GLYCEROL (GOLl)
2m: GLYCEROL (GOLm)
2n: GLYCEROL (GOLn)
2o: GLYCEROL (GOLo)
2p: GLYCEROL (GOLp)
2q: GLYCEROL (GOLq)
2r: GLYCEROL (GOLr)
2s: GLYCEROL (GOLs)
2t: GLYCEROL (GOLt)
2u: GLYCEROL (GOLu)
2v: GLYCEROL (GOLv)
2w: GLYCEROL (GOLw)
2x: GLYCEROL (GOLx)
2y: GLYCEROL (GOLy)
2z: GLYCEROL (GOLz)
3a: PHOSPHATE ION (PO4a)
3b: PHOSPHATE ION (PO4b)
4a: METHIONINE SULFOXIDE (SMEa)
4b: METHIONINE SULFOXIDE (SMEb)
5a: 5-(2-CARBOXY-2-AMINOETHYL)-2-HYDRO... (TPQa)
5b: 5-(2-CARBOXY-2-AMINOETHYL)-2-HYDRO... (TPQb)
5c: 5-(2-CARBOXY-2-AMINOETHYL)-2-HYDRO... (TPQc)
5d: 5-(2-CARBOXY-2-AMINOETHYL)-2-HYDRO... (TPQd)
5e: 5-(2-CARBOXY-2-AMINOETHYL)-2-HYDRO... (TPQe)
5f: 5-(2-CARBOXY-2-AMINOETHYL)-2-HYDRO... (TPQf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CU
6
Ligand/Ion
COPPER (II) ION
2
GOL
28
Ligand/Ion
GLYCEROL
3
PO4
2
Ligand/Ion
PHOSPHATE ION
4
SME
2
Mod. Amino Acid
METHIONINE SULFOXIDE
5
TPQ
6
Mod. Amino Acid
5-(2-CARBOXY-2-AMINOETHYL)-2-HYDROXY-1,4-BENZOQUINONE
[
close Hetero Component info
]
Sites
(36, 36)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:456 , HIS A:458 , HIS A:624 , HOH A:6215
BINDING SITE FOR RESIDUE CU A 801
02
AC2
SOFTWARE
HIS B:456 , HIS B:458 , HIS B:624 , HOH B:6210
BINDING SITE FOR RESIDUE CU B 801
03
AC3
SOFTWARE
TPQ C:405 , HIS C:456 , HIS C:458 , HIS C:624
BINDING SITE FOR RESIDUE CU C 801
04
AC4
SOFTWARE
TPQ D:405 , LEU D:425 , HIS D:456 , HIS D:458 , HIS D:624 , HOH D:6751
BINDING SITE FOR RESIDUE CU D 801
05
AC5
SOFTWARE
TPQ E:405 , HIS E:456 , HIS E:458 , HIS E:624 , HOH E:6752
BINDING SITE FOR RESIDUE CU E 801
06
AC6
SOFTWARE
TPQ F:405 , HIS F:456 , HIS F:458 , HIS F:624
BINDING SITE FOR RESIDUE CU F 801
07
AC7
SOFTWARE
HIS C:218 , LYS C:219 , HOH C:6697 , HOH C:6762 , HOH C:6767
BINDING SITE FOR RESIDUE PO4 C 6010
08
AC8
SOFTWARE
HIS F:218 , LYS F:219 , HOH F:6701 , HOH F:6717
BINDING SITE FOR RESIDUE PO4 F 6011
09
AC9
SOFTWARE
HIS F:23 , TYR F:64 , LYS F:68 , LYS F:265 , ASP F:280 , HOH F:6166 , HOH F:6746
BINDING SITE FOR RESIDUE GOL F 6001
10
BC1
SOFTWARE
LYS C:214 , VAL C:215 , ASP C:436 , HOH C:6215 , HOH C:6429 , HOH C:6812
BINDING SITE FOR RESIDUE GOL C 6002
11
BC2
SOFTWARE
PHE F:51 , ASN F:52 , THR F:117 , GLU F:119 , ASP F:120 , TYR F:327 , SER F:350 , ASP F:351 , ARG F:352 , HOH F:6198
BINDING SITE FOR RESIDUE GOL F 6003
12
BC3
SOFTWARE
ARG B:213 , LYS B:214 , VAL B:215 , ASP B:436 , ASN B:450 , HOH B:6581 , HOH B:6758
BINDING SITE FOR RESIDUE GOL B 6004
13
BC4
SOFTWARE
LYS A:214 , VAL A:215 , ASP A:436 , HOH A:6370
BINDING SITE FOR RESIDUE GOL A 6005
14
BC5
SOFTWARE
LYS F:214 , VAL F:215 , GLY F:435 , ASP F:436 , HOH F:6453
BINDING SITE FOR RESIDUE GOL F 6006
15
BC6
SOFTWARE
LYS C:393 , VAL C:412 , ASP C:422 , ARG C:424 , HOH C:6164 , HOH C:6785 , HOH C:6873
BINDING SITE FOR RESIDUE GOL C 6007
16
BC7
SOFTWARE
GLY E:371 , LYS F:393 , ASP F:422 , ARG F:424 , HOH F:6112 , HOH F:6644 , HOH F:6687
BINDING SITE FOR RESIDUE GOL F 6008
17
BC8
SOFTWARE
GLY A:371 , GLU B:368 , LYS B:393 , TYR B:410 , ARG B:420 , ASP B:422 , ARG B:424 , HOH B:6156 , HOH B:6507 , HOH B:6677 , HOH B:6774
BINDING SITE FOR RESIDUE GOL B 6009
18
BC9
SOFTWARE
GLU A:368 , LYS A:393 , VAL A:412 , ARG A:420 , ASP A:422 , HOH A:6118 , HOH A:6557 , HOH A:6789 , GLY B:371
BINDING SITE FOR RESIDUE GOL A 6012
19
CC1
SOFTWARE
ARG A:61 , LYS A:62 , ASP A:471 , ASP A:613 , HOH A:6623 , HOH A:6707
BINDING SITE FOR RESIDUE GOL A 6013
20
CC2
SOFTWARE
LYS E:214 , VAL E:215 , ASP E:436 , HOH E:6235 , HOH E:6791 , HOH E:6792 , HOH E:6793
BINDING SITE FOR RESIDUE GOL E 6014
21
CC3
SOFTWARE
ASP A:471 , HOH A:6707 , HIS E:218 , LYS E:219 , TYR E:448 , HOH E:6415
BINDING SITE FOR RESIDUE GOL E 6015
22
CC4
SOFTWARE
PRO E:442 , TRP E:443 , PRO F:484 , TYR F:499
BINDING SITE FOR RESIDUE GOL E 6016
23
CC5
SOFTWARE
ARG A:163 , PHE A:310 , HOH A:6315 , HOH A:6442 , HOH A:6632 , HOH A:6844 , HOH B:6144 , ASP F:593 , GLY F:594
BINDING SITE FOR RESIDUE GOL A 6017
24
CC6
SOFTWARE
HIS A:218 , LYS A:219 , TYR A:448 , HOH A:6471
BINDING SITE FOR RESIDUE GOL A 6018
25
CC7
SOFTWARE
LYS E:393 , VAL E:412 , ARG E:420 , ASP E:422 , ARG E:424 , HOH E:6067 , HOH E:6621 , HOH E:6664 , HOH E:6713 , GLY F:371
BINDING SITE FOR RESIDUE GOL E 6019
26
CC8
SOFTWARE
PRO E:484 , PRO F:442
BINDING SITE FOR RESIDUE GOL E 6020
27
CC9
SOFTWARE
HIS C:286 , PHE C:649 , THR C:650 , GLU C:651 , PRO C:653 , GOL C:6029 , HOH C:6125 , HOH C:6181 , HOH C:6294 , HOH C:6530
BINDING SITE FOR RESIDUE GOL C 6021
28
DC1
SOFTWARE
ILE E:208 , PRO E:209 , ASN E:210 , PHE E:310 , HOH E:6131 , HOH E:6282 , HOH E:6674
BINDING SITE FOR RESIDUE GOL E 6022
29
DC2
SOFTWARE
GLY B:142 , PRO B:144 , GLU B:147 , TYR B:177 , HOH B:6704 , HOH D:6484
BINDING SITE FOR RESIDUE GOL B 6023
30
DC3
SOFTWARE
PRO B:484 , TYR B:499 , HOH B:6808
BINDING SITE FOR RESIDUE GOL B 6024
31
DC4
SOFTWARE
GLY B:603 , ASP B:604 , HOH B:6375 , HOH B:6599 , PRO D:490 , GLU D:491
BINDING SITE FOR RESIDUE GOL B 6025
32
DC5
SOFTWARE
HIS B:218 , LYS B:219 , TYR B:448 , HOH B:6275 , HOH B:6757
BINDING SITE FOR RESIDUE GOL B 6026
33
DC6
SOFTWARE
PRO A:484 , TYR A:485 , TYR A:499 , HOH A:6829 , HOH A:6862 , PRO B:442
BINDING SITE FOR RESIDUE GOL A 6027
34
DC7
SOFTWARE
ARG D:20 , PRO D:21 , LEU D:74 , PRO D:75 , ARG D:77 , HOH D:6304 , HOH D:6372 , HOH D:6662 , HOH D:6867
BINDING SITE FOR RESIDUE GOL D 6028
35
DC8
SOFTWARE
GLN B:66 , GLN B:70 , GLY B:72 , TYR C:534 , THR C:650 , GLU C:651 , GOL C:6021 , HOH C:6076 , HOH C:6530 , TYR D:448
BINDING SITE FOR RESIDUE GOL C 6029
36
DC9
SOFTWARE
GLY C:371 , LYS D:393 , VAL D:412 , ARG D:420 , ASP D:422 , ARG D:424 , HOH D:6088 , HOH D:6516 , HOH D:6744 , HOH D:6769
BINDING SITE FOR RESIDUE GOL D 6030
[
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, 12)
Info
All PROSITE Patterns/Profiles
1: COPPER_AMINE_OXID_1 (A:394-407,B:394-407,C:394-407,D:39...)
2: COPPER_AMINE_OXID_2 (A:619-632,B:619-632,C:619-632,D:61...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
COPPER_AMINE_OXID_1
PS01164
Copper amine oxidase topaquinone signature.
AMO_PICAN
394-407
6
A:394-407
B:394-407
C:394-407
D:394-407
E:394-407
F:394-407
2
COPPER_AMINE_OXID_2
PS01165
Copper amine oxidase copper-binding site signature.
AMO_PICAN
619-632
6
A:619-632
B:619-632
C:619-632
D:619-632
E:619-632
F:619-632
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
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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
(2, 18)
Info
All SCOP Domains
1a: SCOP_d2oova1 (A:237-672)
1b: SCOP_d2oove1 (E:237-672)
1c: SCOP_d2oovf1 (F:237-672)
1d: SCOP_d2oovb1 (B:237-672)
1e: SCOP_d2oovc1 (C:237-672)
1f: SCOP_d2oovd1 (D:237-672)
2a: SCOP_d2oova2 (A:18-115)
2b: SCOP_d2oova3 (A:116-236)
2c: SCOP_d2oovb2 (B:18-115)
2d: SCOP_d2oovb3 (B:116-236)
2e: SCOP_d2oovc2 (C:18-115)
2f: SCOP_d2oovc3 (C:116-236)
2g: SCOP_d2oovd2 (D:18-115)
2h: SCOP_d2oovd3 (D:116-236)
2i: SCOP_d2oove2 (E:18-115)
2j: SCOP_d2oove3 (E:116-236)
2k: SCOP_d2oovf2 (F:18-115)
2l: SCOP_d2oovf3 (F:116-236)
View:
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Classes
(
)
(
)
Folds
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(
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Superfamilies
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(
)
Families
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)
(
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Supersandwich
(271)
Superfamily
:
Amine oxidase catalytic domain
(65)
Family
:
Amine oxidase catalytic domain
(65)
Protein domain
:
Copper amine oxidase, domain 3
(62)
Yeast (Hansenula polymorpha) [TaxId: 4905]
(4)
1a
d2oova1
A:237-672
1b
d2oove1
E:237-672
1c
d2oovf1
F:237-672
1d
d2oovb1
B:237-672
1e
d2oovc1
C:237-672
1f
d2oovd1
D:237-672
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Cystatin-like
(403)
Superfamily
:
Amine oxidase N-terminal region
(65)
Family
:
Amine oxidase N-terminal region
(65)
Protein domain
:
Copper amine oxidase, domains 1 and 2
(62)
Yeast (Hansenula polymorpha) [TaxId: 4905]
(4)
2a
d2oova2
A:18-115
2b
d2oova3
A:116-236
2c
d2oovb2
B:18-115
2d
d2oovb3
B:116-236
2e
d2oovc2
C:18-115
2f
d2oovc3
C:116-236
2g
d2oovd2
D:18-115
2h
d2oovd3
D:116-236
2i
d2oove2
E:18-115
2j
d2oove3
E:116-236
2k
d2oovf2
F:18-115
2l
d2oovf3
F:116-236
[
close SCOP info
]
CATH Domains
(2, 18)
Info
all CATH domains
1a: CATH_2oovA01 (A:18-117)
1b: CATH_2oovE01 (E:18-117)
1c: CATH_2oovF01 (F:18-117)
1d: CATH_2oovA02 (A:123-231)
1e: CATH_2oovB02 (B:123-231)
1f: CATH_2oovC02 (C:123-231)
1g: CATH_2oovD02 (D:123-231)
1h: CATH_2oovE02 (E:123-231)
1i: CATH_2oovF02 (F:123-231)
1j: CATH_2oovB01 (B:18-117)
1k: CATH_2oovC01 (C:18-117)
1l: CATH_2oovD01 (D:18-117)
2a: CATH_2oovA03 (A:232-670)
2b: CATH_2oovE03 (E:232-670)
2c: CATH_2oovF03 (F:232-670)
2d: CATH_2oovB03 (B:232-670)
2e: CATH_2oovC03 (C:232-670)
2f: CATH_2oovD03 (D:232-670)
View:
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Architectures
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Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Roll
(3276)
Topology
:
Nuclear Transport Factor 2; Chain: A,
(517)
Homologous Superfamily
:
[code=3.10.450.40, no name defined]
(77)
Pichia angusta. Organism_taxid: 4905.
(2)
1a
2oovA01
A:18-117
1b
2oovE01
E:18-117
1c
2oovF01
F:18-117
1d
2oovA02
A:123-231
1e
2oovB02
B:123-231
1f
2oovC02
C:123-231
1g
2oovD02
D:123-231
1h
2oovE02
E:123-231
1i
2oovF02
F:123-231
1j
2oovB01
B:18-117
1k
2oovC01
C:18-117
1l
2oovD01
D:18-117
Class
:
Mainly Beta
(13760)
Architecture
:
Distorted Sandwich
(506)
Topology
:
Beta-galactosidase; Chain A, domain 5
(250)
Homologous Superfamily
:
Copper amine oxidase, Domain 3
(74)
Pichia angusta. Organism_taxid: 4905.
(2)
2a
2oovA03
A:232-670
2b
2oovE03
E:232-670
2c
2oovF03
F:232-670
2d
2oovB03
B:232-670
2e
2oovC03
C:232-670
2f
2oovD03
D:232-670
[
close CATH info
]
Pfam Domains
(3, 18)
Info
all PFAM domains
1a: PFAM_Cu_amine_oxidN2_2oovF01 (F:23-109)
1b: PFAM_Cu_amine_oxidN2_2oovF02 (F:23-109)
1c: PFAM_Cu_amine_oxidN2_2oovF03 (F:23-109)
1d: PFAM_Cu_amine_oxidN2_2oovF04 (F:23-109)
1e: PFAM_Cu_amine_oxidN2_2oovF05 (F:23-109)
1f: PFAM_Cu_amine_oxidN2_2oovF06 (F:23-109)
2a: PFAM_Cu_amine_oxidN3_2oovF07 (F:114-216)
2b: PFAM_Cu_amine_oxidN3_2oovF08 (F:114-216)
2c: PFAM_Cu_amine_oxidN3_2oovF09 (F:114-216)
2d: PFAM_Cu_amine_oxidN3_2oovF10 (F:114-216)
2e: PFAM_Cu_amine_oxidN3_2oovF11 (F:114-216)
2f: PFAM_Cu_amine_oxidN3_2oovF12 (F:114-216)
3a: PFAM_Cu_amine_oxid_2oovF13 (F:241-662)
3b: PFAM_Cu_amine_oxid_2oovF14 (F:241-662)
3c: PFAM_Cu_amine_oxid_2oovF15 (F:241-662)
3d: PFAM_Cu_amine_oxid_2oovF16 (F:241-662)
3e: PFAM_Cu_amine_oxid_2oovF17 (F:241-662)
3f: PFAM_Cu_amine_oxid_2oovF18 (F:241-662)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
CuAO_N2_N3
(40)
Family
:
Cu_amine_oxidN2
(27)
Pichia angusta (Yeast) (Hansenula polymorpha)
(5)
1a
Cu_amine_oxidN2-2oovF01
F:23-109
1b
Cu_amine_oxidN2-2oovF02
F:23-109
1c
Cu_amine_oxidN2-2oovF03
F:23-109
1d
Cu_amine_oxidN2-2oovF04
F:23-109
1e
Cu_amine_oxidN2-2oovF05
F:23-109
1f
Cu_amine_oxidN2-2oovF06
F:23-109
Family
:
Cu_amine_oxidN3
(37)
Pichia angusta (Yeast) (Hansenula polymorpha)
(5)
2a
Cu_amine_oxidN3-2oovF07
F:114-216
2b
Cu_amine_oxidN3-2oovF08
F:114-216
2c
Cu_amine_oxidN3-2oovF09
F:114-216
2d
Cu_amine_oxidN3-2oovF10
F:114-216
2e
Cu_amine_oxidN3-2oovF11
F:114-216
2f
Cu_amine_oxidN3-2oovF12
F:114-216
Clan
:
no clan defined [family: Cu_amine_oxid]
(40)
Family
:
Cu_amine_oxid
(40)
Pichia angusta (Yeast) (Hansenula polymorpha)
(5)
3a
Cu_amine_oxid-2oovF13
F:241-662
3b
Cu_amine_oxid-2oovF14
F:241-662
3c
Cu_amine_oxid-2oovF15
F:241-662
3d
Cu_amine_oxid-2oovF16
F:241-662
3e
Cu_amine_oxid-2oovF17
F:241-662
3f
Cu_amine_oxid-2oovF18
F:241-662
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