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Getting 'Biological Unit' information from database.
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Getting 'Hetero Component' information from database.
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Getting 'Site' information from database.
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Getting 'PROSITE' information from database.
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Getting 'Exon' information from database.
1DX5
Asym. Unit
Info
Asym.Unit (298 KB)
Biol.Unit 1 (77 KB)
Biol.Unit 2 (77 KB)
Biol.Unit 3 (77 KB)
Biol.Unit 4 (77 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE THROMBIN-THROMBOMODULIN COMPLEX
Authors
:
P. Fuentes-Prior, Y. Iwanaga, R. Huber, R. Pagila, G. Rumennik, M. Seto J. Morser, D. R. Light, W. Bode
Date
:
20 Dec 99 (Deposition) - 10 Apr 00 (Release) - 21 Dec 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1: A,E,I,M (1x)
Biol. Unit 2: B,F,J,N (1x)
Biol. Unit 3: C,G,K,O (1x)
Biol. Unit 4: D,H,L,P (1x)
Keywords
:
Serine Proteinase, Egf-Like Domains, Anticoagulant Complex, Antifibrinolytic Complex, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Fuentes-Prior, Y. Iwanaga, R. Huber, R. Pagila, G. Rumennik, M. Seto, J. Morser, D. R. Light, W. Bode
Structural Basis For The Anticoagulant Activity Of The Thrombin-Thrombomodulin Complex
Nature V. 404 518 2000
[
close entry info
]
Hetero Components
(6, 29)
Info
All Hetero Components
1a: CHLOROMETHANE (0QEa)
1b: CHLOROMETHANE (0QEb)
1c: CHLOROMETHANE (0QEc)
1d: CHLOROMETHANE (0QEd)
2a: AMINO{[(4S)-4-AMINO-5,5-DIHYDROXYP... (AR7a)
2b: AMINO{[(4S)-4-AMINO-5,5-DIHYDROXYP... (AR7b)
2c: AMINO{[(4S)-4-AMINO-5,5-DIHYDROXYP... (AR7c)
2d: AMINO{[(4S)-4-AMINO-5,5-DIHYDROXYP... (AR7d)
3a: CALCIUM ION (CAa)
3b: CALCIUM ION (CAb)
3c: CALCIUM ION (CAc)
3d: CALCIUM ION (CAd)
4a: FORMIC ACID (FMTa)
4b: FORMIC ACID (FMTb)
4c: FORMIC ACID (FMTc)
4d: FORMIC ACID (FMTd)
4e: FORMIC ACID (FMTe)
6a: N-ACETYL-D-GLUCOSAMINE (NAGa)
6b: N-ACETYL-D-GLUCOSAMINE (NAGb)
6c: N-ACETYL-D-GLUCOSAMINE (NAGc)
6d: N-ACETYL-D-GLUCOSAMINE (NAGd)
5a: SODIUM ION (NAa)
5b: SODIUM ION (NAb)
5c: SODIUM ION (NAc)
5d: SODIUM ION (NAd)
5e: SODIUM ION (NAe)
5f: SODIUM ION (NAf)
5g: SODIUM ION (NAg)
6h: SODIUM ION (NAh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
0QE
4
Mod. Amino Acid
CHLOROMETHANE
2
AR7
4
Mod. Amino Acid
AMINO{[(4S)-4-AMINO-5,5-DIHYDROXYPENTYL]AMINO}METHANIMINIUM
3
CA
4
Ligand/Ion
CALCIUM ION
4
FMT
5
Ligand/Ion
FORMIC ACID
5
NA
8
Ligand/Ion
SODIUM ION
6
NAG
4
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(21, 21)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY H:2 , TYR P:60A
BINDING SITE FOR RESIDUE FMT H 502
02
AC2
SOFTWARE
GLU I:357 , NA I:2002
BINDING SITE FOR RESIDUE FMT I 501
03
AC3
SOFTWARE
ASP I:423 , ILE I:424 , GLU I:426 , ASN I:439 , LEU I:440 , THR I:443 , HOH I:2056
BINDING SITE FOR RESIDUE CA I1001
04
AC4
SOFTWARE
TYR I:358 , CYS I:372 , ALA I:373 , CYS I:386 , FMT I:501
BINDING SITE FOR RESIDUE NA I2002
05
AC5
SOFTWARE
GLU J:357 , NA J:2002
BINDING SITE FOR RESIDUE FMT J 501
06
AC6
SOFTWARE
ASP J:423 , ILE J:424 , GLU J:426 , ASN J:439 , LEU J:440 , THR J:443 , HOH J:2059
BINDING SITE FOR RESIDUE CA J1001
07
AC7
SOFTWARE
TYR J:358 , CYS J:372 , ALA J:373 , PHE J:376 , FMT J:501
BINDING SITE FOR RESIDUE NA J2002
08
AC8
SOFTWARE
GLU K:357 , NA K:2002
BINDING SITE FOR RESIDUE FMT K 501
09
AC9
SOFTWARE
ASP K:423 , ILE K:424 , GLU K:426 , ASN K:439 , LEU K:440 , THR K:443 , HOH K:2053
BINDING SITE FOR RESIDUE CA K1001
10
BC1
SOFTWARE
TYR K:358 , CYS K:372 , ALA K:373 , CYS K:386 , FMT K:501
BINDING SITE FOR RESIDUE NA K2002
11
BC2
SOFTWARE
GLU L:357 , NA L:2002
BINDING SITE FOR RESIDUE FMT L 501
12
BC3
SOFTWARE
ASP L:423 , ILE L:424 , GLU L:426 , ASN L:439 , LEU L:440 , THR L:443 , HOH L:2051
BINDING SITE FOR RESIDUE CA L1001
13
BC4
SOFTWARE
TYR L:358 , CYS L:372 , ALA L:373 , PHE L:376 , FMT L:501
BINDING SITE FOR RESIDUE NA L2002
14
BC5
SOFTWARE
ASP M:221 , ARG M:221A , HOH M:2109
BINDING SITE FOR RESIDUE NA M2001
15
BC6
SOFTWARE
ARG N:221A , LYS N:224 , HOH N:2094 , HOH N:2095 , HOH N:2116
BINDING SITE FOR RESIDUE NA N2001
16
BC7
SOFTWARE
ARG O:221A , LYS O:224 , HOH O:2087 , HOH O:2109 , HOH O:2112 , HOH O:2113
BINDING SITE FOR RESIDUE NA O2001
17
BC8
SOFTWARE
ARG P:221A , LYS P:224 , HOH P:2089 , HOH P:2090 , HOH P:2115
BINDING SITE FOR RESIDUE NA P2001
18
BC9
SOFTWARE
LEU M:60 , ASN M:60G , ILE M:60I
BINDING SITE FOR MONO-SACCHARIDE NAG M 600 BOUND TO ASN M 60G
19
CC1
SOFTWARE
LEU N:60 , ASN N:60G , ILE N:60I
BINDING SITE FOR MONO-SACCHARIDE NAG N 600 BOUND TO ASN N 60G
20
CC2
SOFTWARE
ASN O:60G , ILE O:60I
BINDING SITE FOR MONO-SACCHARIDE NAG O 600 BOUND TO ASN O 60G
21
CC3
SOFTWARE
LEU P:60 , ASN P:60G , ILE P:60I , HOH P:2053
BINDING SITE FOR MONO-SACCHARIDE NAG P 600 BOUND TO ASN P 60G
[
close Site info
]
SAPs(SNPs)/Variants
(9, 36)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_006714 (M32T, chain M/N/O/P, )
2: VAR_011782 (P37T, chain M/N/O/P, )
3: VAR_006715 (R67C, chain M/N/O/P, )
4: VAR_006716 (R73H, chain M/N/O/P, )
5: VAR_006717 (R101W, chain M/N/O/P, )
6: VAR_006718 (E146A, chain M/N/O/P, )
7: VAR_068913 (E164Q, chain M/N/O/P, )
8: VAR_006719 (G226V, chain M/N/O/P, )
9: VAR_011370 (A455V, chain I/J/K/L, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_006714
M
380
T
THRB_HUMAN
Disease (FA2D)
---
M/N/O/P
M
32
T
2
UniProt
VAR_011782
P
386
T
THRB_HUMAN
Polymorphism
5897
M/N/O/P
P
37
T
3
UniProt
VAR_006715
R
425
C
THRB_HUMAN
Disease (FA2D)
---
M/N/O/P
R
67
C
4
UniProt
VAR_006716
R
431
H
THRB_HUMAN
Disease (FA2D)
---
M/N/O/P
R
73
H
5
UniProt
VAR_006717
R
461
W
THRB_HUMAN
Disease (FA2D)
---
M/N/O/P
R
101
W
6
UniProt
VAR_006718
E
509
A
THRB_HUMAN
Disease (FA2D)
---
M/N/O/P
E
146
A
7
UniProt
VAR_068913
E
532
Q
THRB_HUMAN
Polymorphism
---
M/N/O/P
E
164
Q
8
UniProt
VAR_006719
G
601
V
THRB_HUMAN
Disease (FA2D)
---
M/N/O/P
G
226
V
9
UniProt
VAR_011370
A
473
V
TRBM_HUMAN
Polymorphism
1042579
I/J/K/L
A
455
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(7, 32)
Info
All PROSITE Patterns/Profiles
1: EGF_3 (-|-|I:347-387,J:347-387,K:347-387,...)
2: EGF_2 (-|I:407-421,J:407-421,K:407-421,L:...)
3: EGF_CA (-|I:423-446,J:423-446,K:423-446,L:...)
4: ASX_HYDROXYL (-|I:437-448,J:437-448,K:437-448,L:...)
5: TRYPSIN_DOM (M:16-243,N:16-243,O:16-243,P:16-24...)
6: TRYPSIN_HIS (M:53-58,N:53-58,O:53-58,P:53-58)
7: TRYPSIN_SER (M:189-200,N:189-200,O:189-200,P:18...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
EGF_3
PS50026
EGF-like domain profile.
TRBM_HUMAN
284-324
325-361
365-405
441-481
8
-
-
I:347-387
J:347-387
K:347-387
L:347-387
I:423-462
J:423-462
K:423-462
L:423-462
2
EGF_2
PS01186
EGF-like domain signature 2.
TRBM_HUMAN
308-323
425-439
4
-
I:407-421
J:407-421
K:407-421
L:407-421
3
EGF_CA
PS01187
Calcium-binding EGF-like domain signature.
TRBM_HUMAN
325-349
441-464
4
-
I:423-446
J:423-446
K:423-446
L:423-446
4
ASX_HYDROXYL
PS00010
Aspartic acid and asparagine hydroxylation site.
TRBM_HUMAN
340-351
455-466
4
-
I:437-448
J:437-448
K:437-448
L:437-448
5
TRYPSIN_DOM
PS50240
Serine proteases, trypsin domain profile.
THRB_HUMAN
364-618
4
M:16-243
N:16-243
O:16-243
P:16-243
6
TRYPSIN_HIS
PS00134
Serine proteases, trypsin family, histidine active site.
THRB_HUMAN
402-407
4
M:53-58
N:53-58
O:53-58
P:53-58
7
TRYPSIN_SER
PS00135
Serine proteases, trypsin family, serine active site.
THRB_HUMAN
562-573
4
M:189-200
N:189-200
O:189-200
P:189-200
[
close PROSITE info
]
Exons
(8, 36)
Info
All Exons
Exon 1.8 (A:1H-1A | B:1H-1A | C:1H-1A | D:1H...)
Exon 1.9 (A:1A-15 | B:1A-15 | C:1A-15 | D:1A...)
Exon 1.10 (- | - | - | - | M:29-75 | N:29-75 ...)
Exon 1.11b (- | - | - | - | M:75-129B | N:75-1...)
Exon 1.12 (- | - | - | - | M:129B-184 | N:129...)
Exon 1.13 (- | - | - | - | M:184-202 | N:184-...)
Exon 1.14c (- | - | - | - | M:203-247 (gaps) |...)
Exon 2.1 (I:345-462 | J:345-462 | K:345-462 ...)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.7b/1.8
02: Boundary 1.8/1.9
03: Boundary 1.9/1.10
04: Boundary 1.10/1.11b
05: Boundary 1.11b/1.12
06: Boundary 1.12/1.13
07: Boundary 1.13/1.14c
08: Boundary 1.14c/-
09: Boundary -/2.1
10: Boundary 2.1/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1a
ENST00000311907
1a
ENSE00001931088
chr11:
46740730-46740864
135
THRB_HUMAN
1-27
27
0
-
-
1.2a
ENST00000311907
2a
ENSE00001181543
chr11:
46741252-46741412
161
THRB_HUMAN
27-80
54
0
-
-
1.3
ENST00000311907
3
ENSE00001181538
chr11:
46742073-46742097
25
THRB_HUMAN
81-89
9
0
-
-
1.4
ENST00000311907
4
ENSE00001181532
chr11:
46742340-46742390
51
THRB_HUMAN
89-106
18
0
-
-
1.6a
ENST00000311907
6a
ENSE00001181527
chr11:
46744730-46744835
106
THRB_HUMAN
106-141
36
0
-
-
1.6c
ENST00000311907
6c
ENSE00001181524
chr11:
46744932-46745068
137
THRB_HUMAN
141-187
47
0
-
-
1.7b
ENST00000311907
7b
ENSE00001688723
chr11:
46747409-46747723
315
THRB_HUMAN
187-292
106
0
-
-
1.8
ENST00000311907
8
ENSE00002179953
chr11:
46748048-46748176
129
THRB_HUMAN
292-335
44
4
A:1H-1A
B:1H-1A
C:1H-1A
D:1H-1A
-
-
-
-
8
8
8
8
-
-
-
-
1.9
ENST00000311907
9
ENSE00001770269
chr11:
46748261-46748387
127
THRB_HUMAN
335-377
43
8
A:1A-15
B:1A-15
C:1A-15
D:1A-15
M:16-29
N:16-29
O:16-29
P:16-29
29
29
29
29
14
14
14
14
1.10
ENST00000311907
10
ENSE00001650441
chr11:
46749546-46749713
168
THRB_HUMAN
377-433
57
4
-
-
-
-
M:29-75
N:29-75
O:29-75
P:29-75
-
-
-
-
57
57
57
57
1.11b
ENST00000311907
11b
ENSE00001657931
chr11:
46750214-46750387
174
THRB_HUMAN
433-491
59
4
-
-
-
-
M:75-129B
N:75-129B
O:75-129B
P:75-129B
-
-
-
-
59
59
59
59
1.12
ENST00000311907
12
ENSE00001646362
chr11:
46750930-46751111
182
THRB_HUMAN
491-552
62
4
-
-
-
-
M:129B-184
N:129B-184
O:129B-184
P:129B-184
-
-
-
-
62
62
62
62
1.13
ENST00000311907
13
ENSE00001680217
chr11:
46760598-46760668
71
THRB_HUMAN
552-575
24
4
-
-
-
-
M:184-202
N:184-202
O:184-202
P:184-202
-
-
-
-
24
24
24
24
1.14c
ENST00000311907
14c
ENSE00001227030
chr11:
46760815-46761056
242
THRB_HUMAN
576-622
47
4
-
-
-
-
M:203-247 (gaps)
N:203-247 (gaps)
O:203-247 (gaps)
P:203-247 (gaps)
-
-
-
-
48
48
48
48
2.1
ENST00000377103
1
ENSE00001472793
chr20:
23030378-23026270
4109
TRBM_HUMAN
1-654
654
4
I:345-462
J:345-462
K:345-462
L:345-462
118
118
118
118
[
close EXON info
]
SCOP Domains
(2, 16)
Info
All SCOP Domains
1a: SCOP_d1dx5_1 (A:,M:)
1b: SCOP_d1dx5_2 (B:,N:)
1c: SCOP_d1dx5_3 (C:,O:)
1d: SCOP_d1dx5_4 (D:,P:)
2a: SCOP_d1dx5i1 (I:345-387)
2b: SCOP_d1dx5i2 (I:388-422)
2c: SCOP_d1dx5l2 (L:388-422)
2d: SCOP_d1dx5l3 (L:423-462)
2e: SCOP_d1dx5i3 (I:423-462)
2f: SCOP_d1dx5j1 (J:345-387)
2g: SCOP_d1dx5j2 (J:388-422)
2h: SCOP_d1dx5j3 (J:423-462)
2i: SCOP_d1dx5k1 (K:345-387)
2j: SCOP_d1dx5k2 (K:388-422)
2k: SCOP_d1dx5k3 (K:423-462)
2l: SCOP_d1dx5l1 (L:345-387)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Trypsin-like serine proteases
(1752)
Superfamily
:
Trypsin-like serine proteases
(1752)
Family
:
Eukaryotic proteases
(1343)
Protein domain
:
Thrombin
(188)
Human (Homo sapiens) [TaxId: 9606]
(169)
1a
d1dx5.1
A:,M:
1b
d1dx5.2
B:,N:
1c
d1dx5.3
C:,O:
1d
d1dx5.4
D:,P:
Class
:
Small proteins
(3458)
Fold
:
Knottins (small inhibitors, toxins, lectins)
(761)
Superfamily
:
EGF/Laminin
(347)
Family
:
EGF-type module
(304)
Protein domain
:
Thrombomodulin, different EGF-like domains
(6)
Human (Homo sapiens) [TaxId: 9606]
(6)
2a
d1dx5i1
I:345-387
2b
d1dx5i2
I:388-422
2c
d1dx5l2
L:388-422
2d
d1dx5l3
L:423-462
2e
d1dx5i3
I:423-462
2f
d1dx5j1
J:345-387
2g
d1dx5j2
J:388-422
2h
d1dx5j3
J:423-462
2i
d1dx5k1
K:345-387
2j
d1dx5k2
K:388-422
2k
d1dx5k3
K:423-462
2l
d1dx5l1
L:345-387
[
close SCOP info
]
CATH Domains
(2, 20)
Info
all CATH domains
1a: CATH_1dx5M02 (M:28-120,M:233-246)
1b: CATH_1dx5M01 (M:16-27,M:121-232)
1c: CATH_1dx5N01 (N:16-27,N:121-232)
1d: CATH_1dx5O01 (O:16-27,O:121-232)
1e: CATH_1dx5P01 (P:16-27,P:121-232)
1f: CATH_1dx5N02 (N:28-120,N:233-246)
1g: CATH_1dx5O02 (O:28-120,O:233-246)
1h: CATH_1dx5P02 (P:28-120,P:233-246)
2a: CATH_1dx5I01 (I:345-389)
2b: CATH_1dx5J01 (J:345-389)
2c: CATH_1dx5K01 (K:345-389)
2d: CATH_1dx5L01 (L:345-389)
2e: CATH_1dx5I03 (I:423-462)
2f: CATH_1dx5J03 (J:423-462)
2g: CATH_1dx5K03 (K:423-462)
2h: CATH_1dx5L03 (L:423-462)
2i: CATH_1dx5I02 (I:390-422)
2j: CATH_1dx5J02 (J:390-422)
2k: CATH_1dx5K02 (K:390-422)
2l: CATH_1dx5L02 (L:390-422)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Thrombin, subunit H
(1535)
Homologous Superfamily
:
Trypsin-like serine proteases
(1488)
Human (Homo sapiens)
(615)
1a
1dx5M02
M:28-120,M:233-246
1b
1dx5M01
M:16-27,M:121-232
1c
1dx5N01
N:16-27,N:121-232
1d
1dx5O01
O:16-27,O:121-232
1e
1dx5P01
P:16-27,P:121-232
1f
1dx5N02
N:28-120,N:233-246
1g
1dx5O02
O:28-120,O:233-246
1h
1dx5P02
P:28-120,P:233-246
Architecture
:
Ribbon
(789)
Topology
:
Laminin
(270)
Homologous Superfamily
:
Laminin
(263)
Human (Homo sapiens)
(195)
2a
1dx5I01
I:345-389
2b
1dx5J01
J:345-389
2c
1dx5K01
K:345-389
2d
1dx5L01
L:345-389
2e
1dx5I03
I:423-462
2f
1dx5J03
J:423-462
2g
1dx5K03
K:423-462
2h
1dx5L03
L:423-462
2i
1dx5I02
I:390-422
2j
1dx5J02
J:390-422
2k
1dx5K02
K:390-422
2l
1dx5L02
L:390-422
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