PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
1H7W
Asym. Unit
Info
Asym.Unit (739 KB)
Biol.Unit 1 (366 KB)
Biol.Unit 2 (370 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
DIHYDROPYRIMIDINE DEHYDROGENASE (DPD) FROM PIG
Authors
:
D. Dobritzsch, G. Schneider, K. D. Schnackerz, Y. Lindqvist
Date
:
19 Jan 01 (Deposition) - 23 Feb 01 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Electron Transfer, Flavin, Iron-Sulfur Clusters, Pyrimidine Catabolism, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Dobritzsch, G. Schneider, K. D. Schnackerz, Y. Lindqvist
Crystal Structure Of Dihydropyrimidine Dehydrogenase, A Major Determinant Of The Pharmacokinetics Of The Anti-Cancer Drug 5-Fluorouracil
Embo J. V. 20 650 2001
[
close entry info
]
Hetero Components
(3, 24)
Info
All Hetero Components
1a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
1b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
1c: FLAVIN-ADENINE DINUCLEOTIDE (FADc)
1d: FLAVIN-ADENINE DINUCLEOTIDE (FADd)
2a: FLAVIN MONONUCLEOTIDE (FMNa)
2b: FLAVIN MONONUCLEOTIDE (FMNb)
2c: FLAVIN MONONUCLEOTIDE (FMNc)
2d: FLAVIN MONONUCLEOTIDE (FMNd)
3a: IRON/SULFUR CLUSTER (SF4a)
3b: IRON/SULFUR CLUSTER (SF4b)
3c: IRON/SULFUR CLUSTER (SF4c)
3d: IRON/SULFUR CLUSTER (SF4d)
3e: IRON/SULFUR CLUSTER (SF4e)
3f: IRON/SULFUR CLUSTER (SF4f)
3g: IRON/SULFUR CLUSTER (SF4g)
3h: IRON/SULFUR CLUSTER (SF4h)
3i: IRON/SULFUR CLUSTER (SF4i)
3j: IRON/SULFUR CLUSTER (SF4j)
3k: IRON/SULFUR CLUSTER (SF4k)
3l: IRON/SULFUR CLUSTER (SF4l)
3m: IRON/SULFUR CLUSTER (SF4m)
3n: IRON/SULFUR CLUSTER (SF4n)
3o: IRON/SULFUR CLUSTER (SF4o)
3p: IRON/SULFUR CLUSTER (SF4p)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FAD
4
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
2
FMN
4
Ligand/Ion
FLAVIN MONONUCLEOTIDE
3
SF4
16
Ligand/Ion
IRON/SULFUR CLUSTER
[
close Hetero Component info
]
Sites
(24, 24)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS A:91 , PRO A:92 , ILE A:97 , ASN A:120 , CYS A:130 , CYS A:136 , GLN A:156
BINDING SITE FOR RESIDUE SF4 A1026
02
AC2
SOFTWARE
CYS A:79 , LEU A:80 , LYS A:81 , CYS A:82 , PRO A:86 , CYS A:87 , CYS A:140 , ASN A:141 , LEU A:142 , ILE A:150 , ILE A:152
BINDING SITE FOR RESIDUE SF4 A1027
03
AC3
SOFTWARE
ILE A:948 , CYS A:953 , ILE A:954 , ASN A:955 , CYS A:956 , GLY A:957 , CYS A:959 , CYS A:996 , PRO A:997 , CYS A:1001
BINDING SITE FOR RESIDUE SF4 A1028
04
AC4
SOFTWARE
CYS A:963 , TYR A:968 , ILE A:971 , CYS A:986 , THR A:987 , GLY A:988 , CYS A:989 , THR A:990 , CYS A:992
BINDING SITE FOR RESIDUE SF4 A1029
05
AC5
SOFTWARE
ALA A:549 , SER A:550 , ALA A:551 , LYS A:574 , THR A:575 , ILE A:590 , ASN A:609 , ASN A:668 , LYS A:709 , THR A:735 , ASN A:736 , SER A:766 , GLY A:767 , THR A:793 , GLY A:794 , GLY A:795 , CYS A:816 , SER A:817 , GLN A:820 , HOH A:2795 , HOH A:2921 , HOH A:3140
BINDING SITE FOR RESIDUE FMN A1030
06
AC6
SOFTWARE
VAL A:129 , GLY A:194 , GLY A:196 , PRO A:197 , ALA A:198 , GLU A:218 , LYS A:219 , GLN A:220 , GLY A:225 , LEU A:226 , GLU A:230 , ARG A:235 , LYS A:259 , SER A:260 , LEU A:261 , GLY A:282 , ILE A:283 , GLY A:284 , LEU A:310 , ASP A:342 , THR A:343 , ASP A:346 , GLY A:480 , ASP A:481 , ASN A:487 , THR A:488 , THR A:489 , SER A:492 , HOH A:2373 , HOH A:3141 , HOH A:3142 , HOH A:3143 , HOH A:3144 , HOH A:3145 , HOH A:3146 , HOH A:3147 , HOH A:3148
BINDING SITE FOR RESIDUE FAD A1031
07
AC7
SOFTWARE
CYS B:91 , PRO B:92 , ILE B:97 , ASN B:120 , CYS B:130 , CYS B:136 , GLN B:156
BINDING SITE FOR RESIDUE SF4 B1026
08
AC8
SOFTWARE
CYS B:79 , LEU B:80 , LYS B:81 , CYS B:82 , PRO B:86 , CYS B:87 , CYS B:140 , ASN B:141 , LEU B:142 , ILE B:150 , ILE B:152
BINDING SITE FOR RESIDUE SF4 B1027
09
AC9
SOFTWARE
ILE B:948 , CYS B:953 , ILE B:954 , CYS B:956 , GLY B:957 , CYS B:959 , CYS B:996 , PRO B:997 , CYS B:1001 , ILE B:1002
BINDING SITE FOR RESIDUE SF4 B1028
10
BC1
SOFTWARE
CYS B:963 , TYR B:968 , ILE B:971 , VAL B:982 , CYS B:986 , THR B:987 , GLY B:988 , CYS B:989 , THR B:990 , CYS B:992
BINDING SITE FOR RESIDUE SF4 B1029
11
BC2
SOFTWARE
ALA B:549 , SER B:550 , ALA B:551 , LYS B:574 , THR B:575 , ILE B:590 , ASN B:609 , ASN B:668 , LYS B:709 , THR B:735 , ASN B:736 , SER B:766 , GLY B:767 , THR B:793 , GLY B:794 , GLY B:795 , CYS B:816 , SER B:817 , GLN B:820 , HOH B:2815 , HOH B:2917 , HOH B:3117
BINDING SITE FOR RESIDUE FMN B1030
12
BC3
SOFTWARE
VAL B:129 , GLY B:194 , GLY B:196 , PRO B:197 , ALA B:198 , GLU B:218 , LYS B:219 , GLN B:220 , GLY B:225 , LEU B:226 , GLU B:230 , ARG B:235 , LYS B:259 , SER B:260 , LEU B:261 , GLY B:282 , ILE B:283 , GLY B:284 , LEU B:310 , THR B:343 , ASP B:346 , GLY B:480 , ASP B:481 , ASN B:487 , THR B:488 , THR B:489 , SER B:492 , HOH B:2367 , HOH B:2370 , HOH B:2640 , HOH B:3119 , HOH B:3120 , HOH B:3121 , HOH B:3122 , HOH B:3123 , HOH B:3124 , HOH B:3125
BINDING SITE FOR RESIDUE FAD B1031
13
BC4
SOFTWARE
CYS C:91 , PRO C:92 , ILE C:97 , ASN C:120 , CYS C:130 , THR C:132 , CYS C:136 , GLN C:156
BINDING SITE FOR RESIDUE SF4 C1026
14
BC5
SOFTWARE
CYS C:79 , LEU C:80 , LYS C:81 , CYS C:82 , PRO C:86 , CYS C:87 , CYS C:140 , ASN C:141 , LEU C:142 , ILE C:150 , ILE C:152
BINDING SITE FOR RESIDUE SF4 C1027
15
BC6
SOFTWARE
ILE C:948 , CYS C:953 , ILE C:954 , CYS C:956 , GLY C:957 , CYS C:959 , CYS C:996 , PRO C:997 , CYS C:1001 , ILE C:1002
BINDING SITE FOR RESIDUE SF4 C1028
16
BC7
SOFTWARE
CYS C:963 , TYR C:968 , ILE C:971 , VAL C:982 , CYS C:986 , THR C:987 , GLY C:988 , CYS C:989 , THR C:990 , CYS C:992
BINDING SITE FOR RESIDUE SF4 C1029
17
BC8
SOFTWARE
ALA C:549 , SER C:550 , ALA C:551 , LYS C:574 , THR C:575 , ILE C:590 , ASN C:609 , ASN C:668 , LYS C:709 , THR C:735 , ASN C:736 , SER C:766 , GLY C:767 , THR C:793 , GLY C:794 , GLY C:795 , CYS C:816 , SER C:817 , GLN C:820 , HOH C:2838 , HOH C:2926 , HOH C:3169
BINDING SITE FOR RESIDUE FMN C1030
18
BC9
SOFTWARE
VAL C:129 , PRO C:131 , GLY C:194 , GLY C:196 , PRO C:197 , ALA C:198 , GLU C:218 , LYS C:219 , GLN C:220 , GLY C:225 , LEU C:226 , GLU C:230 , ARG C:235 , SER C:260 , LEU C:261 , GLY C:282 , ILE C:283 , GLY C:284 , LEU C:310 , ASP C:342 , THR C:343 , ASP C:346 , GLY C:480 , ASP C:481 , ASN C:487 , THR C:488 , THR C:489 , SER C:492 , HOH C:2359 , HOH C:2645 , HOH C:3170 , HOH C:3171 , HOH C:3172 , HOH C:3173 , HOH C:3174 , HOH C:3175 , HOH C:3176
BINDING SITE FOR RESIDUE FAD C1031
19
CC1
SOFTWARE
CYS D:91 , PRO D:92 , ILE D:97 , ASN D:120 , CYS D:130 , THR D:132 , CYS D:136 , GLN D:156
BINDING SITE FOR RESIDUE SF4 D1026
20
CC2
SOFTWARE
CYS D:79 , LEU D:80 , LYS D:81 , CYS D:82 , CYS D:87 , CYS D:140 , ASN D:141 , LEU D:142 , ILE D:150 , ILE D:152
BINDING SITE FOR RESIDUE SF4 D1027
21
CC3
SOFTWARE
ILE D:948 , CYS D:953 , ILE D:954 , CYS D:956 , GLY D:957 , LYS D:958 , CYS D:959 , CYS D:996 , PRO D:997 , CYS D:1001 , ILE D:1002
BINDING SITE FOR RESIDUE SF4 D1028
22
CC4
SOFTWARE
CYS D:963 , TYR D:968 , ILE D:971 , CYS D:986 , THR D:987 , GLY D:988 , CYS D:989 , THR D:990 , CYS D:992
BINDING SITE FOR RESIDUE SF4 D1029
23
CC5
SOFTWARE
ALA D:549 , SER D:550 , ALA D:551 , LYS D:574 , THR D:575 , ILE D:590 , ASN D:609 , ASN D:668 , LYS D:709 , THR D:735 , ASN D:736 , SER D:766 , GLY D:767 , THR D:793 , GLY D:794 , GLY D:795 , CYS D:816 , SER D:817 , GLN D:820 , HOH D:2847 , HOH D:2994 , HOH D:3182
BINDING SITE FOR RESIDUE FMN D1030
24
CC6
SOFTWARE
VAL D:129 , GLY D:194 , GLY D:196 , PRO D:197 , ALA D:198 , GLU D:218 , LYS D:219 , GLN D:220 , GLY D:225 , LEU D:226 , GLU D:230 , ARG D:235 , LYS D:259 , SER D:260 , LEU D:261 , GLY D:282 , ILE D:283 , GLY D:284 , LEU D:310 , THR D:343 , ASP D:346 , GLY D:480 , ASP D:481 , ASN D:487 , THR D:488 , THR D:489 , SER D:492 , HOH D:2397 , HOH D:2703 , HOH D:3183 , HOH D:3184 , HOH D:3185 , HOH D:3186 , HOH D:3187 , HOH D:3189 , HOH D:3190
BINDING SITE FOR RESIDUE FAD D1031
[
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, 16)
Info
All PROSITE Patterns/Profiles
1: 4FE4S_FER_2 (A:69-100,B:69-100,C:69-100,D:69-10...)
2: 4FE4S_FER_1 (A:986-997,B:986-997,C:986-997,D:98...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
4FE4S_FER_2
PS51379
4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
DPYD_PIG
69-100
944-976
978-1007
12
A:69-100
B:69-100
C:69-100
D:69-100
A:944-976
B:944-976
C:944-976
D:944-976
A:978-1007
B:978-1007
C:978-1007
D:978-1007
2
4FE4S_FER_1
PS00198
4Fe-4S ferredoxin-type iron-sulfur binding region signature.
DPYD_PIG
986-997
4
A:986-997
B:986-997
C:986-997
D:986-997
[
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
(5, 20)
Info
All SCOP Domains
1a: SCOP_d1h7wa1 (A:2-183)
1b: SCOP_d1h7wb1 (B:2-183)
1c: SCOP_d1h7wc1 (C:2-183)
1d: SCOP_d1h7wd1 (D:2-183)
2a: SCOP_d1h7wa5 (A:845-1017)
2b: SCOP_d1h7wb5 (B:845-1018)
2c: SCOP_d1h7wc5 (C:845-1017)
2d: SCOP_d1h7wd5 (D:845-1019)
3a: SCOP_d1h7wa3 (A:288-440)
3b: SCOP_d1h7wb3 (B:288-440)
3c: SCOP_d1h7wc3 (C:288-440)
3d: SCOP_d1h7wd3 (D:288-440)
4a: SCOP_d1h7wa4 (A:184-287,A:441-532)
4b: SCOP_d1h7wb4 (B:184-287,B:441-532)
4c: SCOP_d1h7wc4 (C:184-287,C:441-532)
4d: SCOP_d1h7wd4 (D:184-287,D:441-532)
5a: SCOP_d1h7wa2 (A:533-844)
5b: SCOP_d1h7wb2 (B:533-844)
5c: SCOP_d1h7wc2 (C:533-844)
5d: SCOP_d1h7wd2 (D:533-844)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Globin-like
(1351)
Superfamily
:
alpha-helical ferredoxin
(43)
Family
:
Dihydropyrimidine dehydrogenase, N-terminal domain
(5)
Protein domain
:
Dihydropyrimidine dehydrogenase, N-terminal domain
(5)
Pig (Sus scrofa) [TaxId: 9823]
(5)
1a
d1h7wa1
A:2-183
1b
d1h7wb1
B:2-183
1c
d1h7wc1
C:2-183
1d
d1h7wd1
D:2-183
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
4Fe-4S ferredoxins
(143)
Family
:
Ferredoxin domains from multidomain proteins
(69)
Protein domain
:
Dihydropyrimidine dehydrogenase, C-terminal domain
(5)
Pig (Sus scrofa) [TaxId: 9823]
(5)
2a
d1h7wa5
A:845-1017
2b
d1h7wb5
B:845-1018
2c
d1h7wc5
C:845-1017
2d
d1h7wd5
D:845-1019
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
FAD/NAD(P)-binding domain
(331)
Superfamily
:
FAD/NAD(P)-binding domain
(331)
Family
:
C-terminal domain of adrenodoxin reductase-like
(19)
Protein domain
:
Dihydropyrimidine dehydrogenase, domain 3
(5)
Pig (Sus scrofa) [TaxId: 9823]
(5)
3a
d1h7wa3
A:288-440
3b
d1h7wb3
B:288-440
3c
d1h7wc3
C:288-440
3d
d1h7wd3
D:288-440
Fold
:
Nucleotide-binding domain
(33)
Superfamily
:
Nucleotide-binding domain
(33)
Family
:
N-terminal domain of adrenodoxin reductase-like
(19)
Protein domain
:
Dihydropyrimidine dehydrogenase, domain 2
(5)
Pig (Sus scrofa) [TaxId: 9823]
(5)
4a
d1h7wa4
A:184-287,A:441-532
4b
d1h7wb4
B:184-287,B:441-532
4c
d1h7wc4
C:184-287,C:441-532
4d
d1h7wd4
D:184-287,D:441-532
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
FMN-linked oxidoreductases
(290)
Family
:
FMN-linked oxidoreductases
(242)
Protein domain
:
Dihydropyrimidine dehydrogenase, domain 4
(5)
Pig (Sus scrofa) [TaxId: 9823]
(5)
5a
d1h7wa2
A:533-844
5b
d1h7wb2
B:533-844
5c
d1h7wc2
C:533-844
5d
d1h7wd2
D:533-844
[
close SCOP info
]
CATH Domains
(4, 20)
Info
all CATH domains
1a: CATH_1h7wA01 (A:2-26,A:934-1017)
1b: CATH_1h7wC01 (C:2-26,C:934-1017)
1c: CATH_1h7wB01 (B:2-26,B:934-1018)
1d: CATH_1h7wD01 (D:2-26,D:934-1019)
2a: CATH_1h7wA03 (A:184-287,A:441-532)
2b: CATH_1h7wB03 (B:184-287,B:441-532)
2c: CATH_1h7wC04 (C:288-440)
2d: CATH_1h7wD04 (D:288-440)
2e: CATH_1h7wC03 (C:184-287,C:441-532)
2f: CATH_1h7wD03 (D:184-287,D:441-532)
2g: CATH_1h7wA04 (A:288-440)
2h: CATH_1h7wB04 (B:288-440)
3a: CATH_1h7wA05 (A:533-844)
3b: CATH_1h7wB05 (B:533-844)
3c: CATH_1h7wC05 (C:533-844)
3d: CATH_1h7wD05 (D:533-844)
4a: CATH_1h7wA02 (A:27-183)
4b: CATH_1h7wB02 (B:27-183)
4c: CATH_1h7wC02 (C:27-183)
4d: CATH_1h7wD02 (D:27-183)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.20, no name defined]
(120)
Wild boar (Sus scrofa)
(2)
1a
1h7wA01
A:2-26,A:934-1017
1b
1h7wC01
C:2-26,C:934-1017
1c
1h7wB01
B:2-26,B:934-1018
1d
1h7wD01
D:2-26,D:934-1019
Architecture
:
3-Layer(bba) Sandwich
(528)
Topology
:
FAD/NAD(P)-binding domain
(373)
Homologous Superfamily
:
[code=3.50.50.60, no name defined]
(373)
Wild boar (Sus scrofa)
(2)
2a
1h7wA03
A:184-287,A:441-532
2b
1h7wB03
B:184-287,B:441-532
2c
1h7wC04
C:288-440
2d
1h7wD04
D:288-440
2e
1h7wC03
C:184-287,C:441-532
2f
1h7wD03
D:184-287,D:441-532
2g
1h7wA04
A:288-440
2h
1h7wB04
B:288-440
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Aldolase class I
(887)
Wild boar (Sus scrofa)
(2)
3a
1h7wA05
A:533-844
3b
1h7wB05
B:533-844
3c
1h7wC05
C:533-844
3d
1h7wD05
D:533-844
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2
(33)
Homologous Superfamily
:
Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2
(33)
Wild boar (Sus scrofa)
(2)
4a
1h7wA02
A:27-183
4b
1h7wB02
B:27-183
4c
1h7wC02
C:27-183
4d
1h7wD02
D:27-183
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
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)
[
close Script example commands
]
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") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (739 KB)
Header - Asym.Unit
Biol.Unit 1 (366 KB)
Header - Biol.Unit 1
Biol.Unit 2 (370 KB)
Header - Biol.Unit 2
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
1H7W
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
