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1JRO
Biol. Unit 1
Info
Asym.Unit (751 KB)
Biol.Unit 1 (375 KB)
Biol.Unit 2 (377 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF XANTHINE DEHYDROGENASE FROM RHODOBACTER CAPSULATUS
Authors
:
J. J. Truglio, K. Theis, S. Leimkuhler, R. Rappa, K. V. Rajagopalan, C. K
Date
:
14 Aug 01 (Deposition) - 11 Jan 02 (Release) - 22 Apr 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Keywords
:
Partial Beta-Barrel; Xdh; Xo, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. J. Truglio, K. Theis, S. Leimkuhler, R. Rappa, K. V. Rajagopalan, C. Kisker
Crystal Structures Of The Active And Alloxanthine-Inhibited Forms Of Xanthine Dehydrogenase From Rhodobacter Capsulatus
Structure V. 10 115 2002
[
close entry info
]
Hetero Components
(4, 10)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
2b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
2c: FLAVIN-ADENINE DINUCLEOTIDE (FADc)
2d: FLAVIN-ADENINE DINUCLEOTIDE (FADd)
3a: FE2/S2 (INORGANIC) CLUSTER (FESa)
3b: FE2/S2 (INORGANIC) CLUSTER (FESb)
3c: FE2/S2 (INORGANIC) CLUSTER (FESc)
3d: FE2/S2 (INORGANIC) CLUSTER (FESd)
3e: FE2/S2 (INORGANIC) CLUSTER (FESe)
3f: FE2/S2 (INORGANIC) CLUSTER (FESf)
3g: FE2/S2 (INORGANIC) CLUSTER (FESg)
3h: FE2/S2 (INORGANIC) CLUSTER (FESh)
4a: DIOXOTHIOMOLYBDENUM(VI) ION (MOSa)
4b: DIOXOTHIOMOLYBDENUM(VI) ION (MOSb)
4c: DIOXOTHIOMOLYBDENUM(VI) ION (MOSc)
4d: DIOXOTHIOMOLYBDENUM(VI) ION (MOSd)
5a: PHOSPHONIC ACIDMONO-(2-AMINO-5,6-D... (MTEa)
5b: PHOSPHONIC ACIDMONO-(2-AMINO-5,6-D... (MTEb)
5c: PHOSPHONIC ACIDMONO-(2-AMINO-5,6-D... (MTEc)
5d: PHOSPHONIC ACIDMONO-(2-AMINO-5,6-D... (MTEd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
3
FES
4
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
4
MOS
2
Ligand/Ion
DIOXOTHIOMOLYBDENUM(VI) ION
5
MTE
2
Ligand/Ion
PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER
[
close Hetero Component info
]
Sites
(12, 12)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC5 (SOFTWARE)
04: AC6 (SOFTWARE)
05: AC7 (SOFTWARE)
06: AC8 (SOFTWARE)
07: AC9 (SOFTWARE)
08: BC1 (SOFTWARE)
09: BC2 (SOFTWARE)
10: BC3 (SOFTWARE)
11: BC4 (SOFTWARE)
12: BC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU B:172 , HIS B:173 , TYR B:175 , THR B:266 , GLY B:267
BINDING SITE FOR RESIDUE CA B 3006
02
AC2
SOFTWARE
GLU D:172 , HIS D:173 , TYR D:175 , THR D:266 , GLY D:267
BINDING SITE FOR RESIDUE CA D 3006
03
AC5
SOFTWARE
GLN A:102 , CYS A:103 , GLY A:104 , CYS A:106 , CYS A:134 , ARG A:135 , CYS A:136
BINDING SITE FOR RESIDUE FES A 3001
04
AC6
SOFTWARE
GLY A:38 , CYS A:39 , ASN A:40 , GLY A:42 , CYS A:44 , GLY A:45 , CYS A:47 , ASN A:61 , CYS A:63
BINDING SITE FOR RESIDUE FES A 3002
05
AC7
SOFTWARE
GLN A:102 , CYS A:136 , GLY B:226 , GLY B:227 , PHE B:228 , ARG B:342 , MET B:488 , GLY B:489 , GLN B:490 , THR B:527 , ALA B:528 , ALA B:529 , SER B:530 , SER B:531 , GLY B:532 , ALA B:533 , GLN B:663 , GLU B:730 , MOS B:3004
BINDING SITE FOR RESIDUE MTE B 3003
06
AC8
SOFTWARE
GLN B:197 , GLY B:229 , PHE B:341 , ARG B:342 , ALA B:528 , ALA B:529 , GLU B:730 , MTE B:3003
BINDING SITE FOR RESIDUE MOS B 3004
07
AC9
SOFTWARE
GLU A:41 , GLY A:42 , ASP A:43 , LEU A:201 , ALA A:203 , GLY A:204 , GLY A:205 , THR A:206 , ASP A:207 , VAL A:208 , TRP A:211 , PHE A:270 , ALA A:271 , ALA A:279 , THR A:280 , GLY A:283 , ASN A:284 , ALA A:286 , GLY A:292 , ASP A:293 , ARG A:330 , PHE A:335 , VAL A:336 , LYS A:352 , GLN A:359
BINDING SITE FOR RESIDUE FAD A 3005
08
BC1
SOFTWARE
GLN C:102 , CYS C:103 , GLY C:104 , CYS C:106 , CYS C:134 , ARG C:135 , CYS C:136
BINDING SITE FOR RESIDUE FES C 3001
09
BC2
SOFTWARE
GLY C:38 , CYS C:39 , ASN C:40 , GLY C:42 , CYS C:44 , GLY C:45 , CYS C:47 , CYS C:63
BINDING SITE FOR RESIDUE FES C 3002
10
BC3
SOFTWARE
GLN C:102 , CYS C:136 , GLY D:226 , GLY D:227 , PHE D:228 , ARG D:342 , MET D:488 , GLY D:489 , GLN D:490 , THR D:527 , ALA D:528 , ALA D:529 , SER D:530 , SER D:531 , GLY D:532 , ALA D:533 , GLN D:663 , GLU D:730 , MOS D:3004
BINDING SITE FOR RESIDUE MTE D 3003
11
BC4
SOFTWARE
GLN D:197 , GLY D:229 , PHE D:341 , ARG D:342 , ALA D:528 , ALA D:529 , GLU D:730 , MTE D:3003
BINDING SITE FOR RESIDUE MOS D 3004
12
BC5
SOFTWARE
GLU C:41 , GLY C:42 , ASP C:43 , LEU C:201 , ALA C:203 , GLY C:204 , GLY C:205 , THR C:206 , ASP C:207 , VAL C:208 , PHE C:270 , ALA C:271 , ALA C:279 , THR C:280 , ASN C:284 , ALA C:286 , GLY C:292 , ASP C:293 , ARG C:330 , PHE C:335 , VAL C:336 , LYS C:352 , GLN C:359
BINDING SITE FOR RESIDUE FAD C 3005
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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End label:
Sorry, no Info available
[
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]
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(6, 24)
Info
All SCOP Domains
1a: SCOP_d1jroa1 (A:85-166)
1b: SCOP_d1jroc1 (C:85-166)
1c: SCOP_d1jroe1 (E:85-166)
1d: SCOP_d1jrog1 (G:85-166)
2a: SCOP_d1jrob1 (B:2-123)
2b: SCOP_d1jrod1 (D:2-123)
2c: SCOP_d1jrof1 (F:2-123)
2d: SCOP_d1jroh1 (H:2-123)
3a: SCOP_d1jroa2 (A:1-84)
3b: SCOP_d1jroc2 (C:1-84)
3c: SCOP_d1jroe2 (E:1-84)
3d: SCOP_d1jrog2 (G:1-84)
4a: SCOP_d1jroa3 (A:346-462)
4b: SCOP_d1jroc3 (C:346-462)
4c: SCOP_d1jroe3 (E:346-462)
4d: SCOP_d1jrog3 (G:346-462)
5a: SCOP_d1jroa4 (A:179-345)
5b: SCOP_d1jroc4 (C:179-345)
5c: SCOP_d1jroe4 (E:179-345)
5d: SCOP_d1jrog4 (G:179-345)
6a: SCOP_d1jrob2 (B:124-777)
6b: SCOP_d1jrod2 (D:124-777)
6c: SCOP_d1jrof2 (F:124-777)
6d: SCOP_d1jroh2 (H:124-777)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
CO dehydrogenase ISP C-domain like
(45)
Superfamily
:
CO dehydrogenase ISP C-domain like
(45)
Family
:
CO dehydrogenase ISP C-domain like
(42)
Protein domain
:
Xanthine dehydrogenase chain A, domain 2
(2)
Rhodobacter capsulatus [TaxId: 1061]
(2)
1a
d1jroa1
A:85-166
1b
d1jroc1
C:85-166
1c
d1jroe1
E:85-166
1d
d1jrog1
G:85-166
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
alpha/beta-Hammerhead
(191)
Superfamily
:
CO dehydrogenase molybdoprotein N-domain-like
(44)
Family
:
CO dehydrogenase molybdoprotein N-domain-like
(34)
Protein domain
:
Xanthine dehydrogenase chain B, N-terminal domain
(4)
Rhodobacter capsulatus [TaxId: 1061]
(4)
2a
d1jrob1
B:2-123
2b
d1jrod1
D:2-123
2c
d1jrof1
F:2-123
2d
d1jroh1
H:2-123
Fold
:
beta-Grasp (ubiquitin-like)
(1032)
Superfamily
:
2Fe-2S ferredoxin-like
(174)
Family
:
2Fe-2S ferredoxin domains from multidomain proteins
(82)
Protein domain
:
Xanthine dehydrogenase chain A, N-terminal domain
(2)
Rhodobacter capsulatus [TaxId: 1061]
(2)
3a
d1jroa2
A:1-84
3b
d1jroc2
C:1-84
3c
d1jroe2
E:1-84
3d
d1jrog2
G:1-84
Fold
:
CO dehydrogenase flavoprotein C-domain-like
(111)
Superfamily
:
CO dehydrogenase flavoprotein C-terminal domain-like
(35)
Family
:
CO dehydrogenase flavoprotein C-terminal domain-like
(23)
Protein domain
:
Xanthine dehydrogenase chain A, domain 4
(2)
Rhodobacter capsulatus [TaxId: 1061]
(2)
4a
d1jroa3
A:346-462
4b
d1jroc3
C:346-462
4c
d1jroe3
E:346-462
4d
d1jrog3
G:346-462
Fold
:
FAD-binding/transporter-associated domain-like
(99)
Superfamily
:
FAD-binding/transporter-associated domain-like
(99)
Family
:
CO dehydrogenase flavoprotein N-terminal domain-like
(33)
Protein domain
:
Xanthine dehydrogenase chain A, domain 3
(2)
Rhodobacter capsulatus [TaxId: 1061]
(2)
5a
d1jroa4
A:179-345
5b
d1jroc4
C:179-345
5c
d1jroe4
E:179-345
5d
d1jrog4
G:179-345
Fold
:
Molybdenum cofactor-binding domain
(44)
Superfamily
:
Molybdenum cofactor-binding domain
(44)
Family
:
Molybdenum cofactor-binding domain
(44)
Protein domain
:
Xanthine dehydrogenase chain B, C-terminal domain
(4)
Rhodobacter capsulatus [TaxId: 1061]
(4)
6a
d1jrob2
B:124-777
6b
d1jrod2
D:124-777
6c
d1jrof2
F:124-777
6d
d1jroh2
H:124-777
[
close SCOP info
]
CATH Domains
(7, 40)
Info
all CATH domains
1a: CATH_1jroB04 (B:138-172,B:267-408)
1b: CATH_1jroD04 (D:138-172,D:267-408)
1c: CATH_1jroF02 (F:461-619)
1d: CATH_1jroH02 (H:461-619)
1e: CATH_1jroB03 (B:411-460,B:620-776)
1f: CATH_1jroD03 (D:411-460,D:620-776)
1g: CATH_1jroF03 (F:411-460,F:620-776)
1h: CATH_1jroH03 (H:411-460,H:620-776)
1i: CATH_1jroF04 (F:138-172,F:267-408)
1j: CATH_1jroB05 (B:173-266)
1k: CATH_1jroD05 (D:173-266)
1l: CATH_1jroF05 (F:173-266)
1m: CATH_1jroH05 (H:173-266)
1n: CATH_1jroH04 (H:138-172,H:267-408)
1o: CATH_1jroB02 (B:461-619)
1p: CATH_1jroD02 (D:461-619)
2a: CATH_1jroA05 (A:349-452)
2b: CATH_1jroC05 (C:349-452)
2c: CATH_1jroE05 (E:349-452)
2d: CATH_1jroG05 (G:349-452)
3a: CATH_1jroA03 (A:181-230)
3b: CATH_1jroC03 (C:181-230)
3c: CATH_1jroE03 (E:181-230)
3d: CATH_1jroG03 (G:181-230)
4a: CATH_1jroA04 (A:231-344)
4b: CATH_1jroC04 (C:231-344)
4c: CATH_1jroE04 (E:231-344)
4d: CATH_1jroG04 (G:231-344)
5a: CATH_1jroB01 (B:2-124)
5b: CATH_1jroD01 (D:2-124)
5c: CATH_1jroF01 (F:2-124)
5d: CATH_1jroH01 (H:2-124)
6a: CATH_1jroA01 (A:1-80)
6b: CATH_1jroC01 (C:1-80)
6c: CATH_1jroE01 (E:1-80)
6d: CATH_1jroG01 (G:1-80)
7a: CATH_1jroA02 (A:81-166)
7b: CATH_1jroC02 (C:81-166)
7c: CATH_1jroE02 (E:81-166)
7d: CATH_1jroG02 (G:81-166)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Aldehyde Oxidoreductase; domain 4
(20)
Homologous Superfamily
:
Aldehyde Oxidoreductase; domain 4
(20)
Rhodobacter capsulatus. Organism_taxid: 1061.
(2)
1a
1jroB04
B:138-172,B:267-408
1b
1jroD04
D:138-172,D:267-408
1c
1jroF02
F:461-619
1d
1jroH02
H:461-619
1e
1jroB03
B:411-460,B:620-776
1f
1jroD03
D:411-460,D:620-776
1g
1jroF03
F:411-460,F:620-776
1h
1jroH03
H:411-460,H:620-776
1i
1jroF04
F:138-172,F:267-408
1j
1jroB05
B:173-266
1k
1jroD05
D:173-266
1l
1jroF05
F:173-266
1m
1jroH05
H:173-266
1n
1jroH04
H:138-172,H:267-408
1o
1jroB02
B:461-619
1p
1jroD02
D:461-619
Topology
:
Enolase-like; domain 1
(252)
Homologous Superfamily
:
[code=3.30.390.50, no name defined]
(22)
Rhodobacter capsulatus. Organism_taxid: 1061.
(6)
2a
1jroA05
A:349-452
2b
1jroC05
C:349-452
2c
1jroE05
E:349-452
2d
1jroG05
G:349-452
Topology
:
Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
(50)
Homologous Superfamily
:
Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2
(50)
Rhodobacter capsulatus. Organism_taxid: 1061.
(6)
3a
1jroA03
A:181-230
3b
1jroC03
C:181-230
3c
1jroE03
E:181-230
3d
1jroG03
G:181-230
Topology
:
Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
(63)
Homologous Superfamily
:
[code=3.30.465.10, no name defined]
(63)
Rhodobacter capsulatus. Organism_taxid: 1061.
(6)
4a
1jroA04
A:231-344
4b
1jroC04
C:231-344
4c
1jroE04
E:231-344
4d
1jroG04
G:231-344
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Aldehyde Oxidoreductase; domain 3
(111)
Homologous Superfamily
:
[code=3.90.1170.50, no name defined]
(20)
Rhodobacter capsulatus. Organism_taxid: 1061.
(2)
5a
1jroB01
B:2-124
5b
1jroD01
D:2-124
5c
1jroF01
F:2-124
5d
1jroH01
H:2-124
Architecture
:
Roll
(3276)
Topology
:
Ubiquitin-like (UB roll)
(674)
Homologous Superfamily
:
[code=3.10.20.30, no name defined]
(153)
Rhodobacter capsulatus. Organism_taxid: 1061.
(6)
6a
1jroA01
A:1-80
6b
1jroC01
C:1-80
6c
1jroE01
E:1-80
6d
1jroG01
G:1-80
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
DNA polymerase; domain 1
(617)
Homologous Superfamily
:
[code=1.10.150.120, no name defined]
(29)
Rhodobacter capsulatus. Organism_taxid: 1061.
(6)
7a
1jroA02
A:81-166
7b
1jroC02
C:81-166
7c
1jroE02
E:81-166
7d
1jroG02
G:81-166
[
close CATH info
]
Pfam Domains
(6, 24)
Info
all PFAM domains
1a: PFAM_FAD_binding_5_1jroG01 (G:179-344)
1b: PFAM_FAD_binding_5_1jroG02 (G:179-344)
1c: PFAM_FAD_binding_5_1jroG03 (G:179-344)
1d: PFAM_FAD_binding_5_1jroG04 (G:179-344)
2a: PFAM_Fer2_1jroG05 (G:5-68)
2b: PFAM_Fer2_1jroG06 (G:5-68)
2c: PFAM_Fer2_1jroG07 (G:5-68)
2d: PFAM_Fer2_1jroG08 (G:5-68)
3a: PFAM_Fer2_2_1jroG09 (G:77-148)
3b: PFAM_Fer2_2_1jroG10 (G:77-148)
3c: PFAM_Fer2_2_1jroG11 (G:77-148)
3d: PFAM_Fer2_2_1jroG12 (G:77-148)
4a: PFAM_Ald_Xan_dh_C2_1jroH01 (H:132-705)
4b: PFAM_Ald_Xan_dh_C2_1jroH02 (H:132-705)
4c: PFAM_Ald_Xan_dh_C2_1jroH03 (H:132-705)
4d: PFAM_Ald_Xan_dh_C2_1jroH04 (H:132-705)
5a: PFAM_Ald_Xan_dh_C_1jroH05 (H:17-124)
5b: PFAM_Ald_Xan_dh_C_1jroH06 (H:17-124)
5c: PFAM_Ald_Xan_dh_C_1jroH07 (H:17-124)
5d: PFAM_Ald_Xan_dh_C_1jroH08 (H:17-124)
6a: PFAM_CO_deh_flav_C_1jroG13 (G:349-450)
6b: PFAM_CO_deh_flav_C_1jroG14 (G:349-450)
6c: PFAM_CO_deh_flav_C_1jroG15 (G:349-450)
6d: PFAM_CO_deh_flav_C_1jroG16 (G:349-450)
View:
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Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
FAD_PCMH
(53)
Family
:
FAD_binding_5
(22)
Rhodobacter capsulatus (Rhodopseudomonas capsulata)
(6)
1a
FAD_binding_5-1jroG01
G:179-344
1b
FAD_binding_5-1jroG02
G:179-344
1c
FAD_binding_5-1jroG03
G:179-344
1d
FAD_binding_5-1jroG04
G:179-344
Clan
:
Fer2
(69)
Family
:
Fer2
(60)
Rhodobacter capsulatus (Rhodopseudomonas capsulata)
(7)
2a
Fer2-1jroG05
G:5-68
2b
Fer2-1jroG06
G:5-68
2c
Fer2-1jroG07
G:5-68
2d
Fer2-1jroG08
G:5-68
Family
:
Fer2_2
(24)
Rhodobacter capsulatus (Rhodopseudomonas capsulata)
(6)
3a
Fer2_2-1jroG09
G:77-148
3b
Fer2_2-1jroG10
G:77-148
3c
Fer2_2-1jroG11
G:77-148
3d
Fer2_2-1jroG12
G:77-148
Clan
:
no clan defined [family: Ald_Xan_dh_C2]
(24)
Family
:
Ald_Xan_dh_C2
(24)
Rhodobacter capsulatus (Rhodopseudomonas capsulata)
(6)
4a
Ald_Xan_dh_C2-1jroH01
H:132-705
4b
Ald_Xan_dh_C2-1jroH02
H:132-705
4c
Ald_Xan_dh_C2-1jroH03
H:132-705
4d
Ald_Xan_dh_C2-1jroH04
H:132-705
Clan
:
no clan defined [family: Ald_Xan_dh_C]
(24)
Family
:
Ald_Xan_dh_C
(24)
Rhodobacter capsulatus (Rhodopseudomonas capsulata)
(6)
5a
Ald_Xan_dh_C-1jroH05
H:17-124
5b
Ald_Xan_dh_C-1jroH06
H:17-124
5c
Ald_Xan_dh_C-1jroH07
H:17-124
5d
Ald_Xan_dh_C-1jroH08
H:17-124
Clan
:
no clan defined [family: CO_deh_flav_C]
(22)
Family
:
CO_deh_flav_C
(22)
Rhodobacter capsulatus (Rhodopseudomonas capsulata)
(6)
6a
CO_deh_flav_C-1jroG13
G:349-450
6b
CO_deh_flav_C-1jroG14
G:349-450
6c
CO_deh_flav_C-1jroG15
G:349-450
6d
CO_deh_flav_C-1jroG16
G:349-450
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