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1HBU
Asym. Unit
Info
Asym.Unit (450 KB)
Biol.Unit 1 (437 KB)
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(1)
Title
:
METHYL-COENZYME M REDUCTASE IN THE MCR-RED1-SILENT STATE IN COMPLEX WITH COENZYME M
Authors
:
U. Ermler, W. Grabarse
Date
:
20 Apr 01 (Deposition) - 16 Aug 01 (Release) - 05 Jul 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Methanogenesis, Biological Methanogenesis, Ni-Enzyme, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
W. Grabarse, F. Mahlert, E. C. Duin, M. Goubeaud, S. Shima, R. K. Thauer V. Lamzin, U. Ermler
On The Mechanism Of Biological Methane Formation: Structura Evidence For Conformational Changes In Methyl-Coenzyme M Reductase Upon Substrate Binding
J. Mol. Biol. V. 309 315 2001
[
close entry info
]
Hetero Components
(13, 52)
Info
All Hetero Components
01a: 5-METHYL-ARGININE (AGMa)
01b: 5-METHYL-ARGININE (AGMb)
02a: CHLORIDE ION (CLa)
02b: CHLORIDE ION (CLb)
03a: 1-THIOETHANESULFONIC ACID (COMa)
03b: 1-THIOETHANESULFONIC ACID (COMb)
04a: FACTOR 430 (F43a)
04b: FACTOR 430 (F43b)
05a: THIOGLYCIN (GL3a)
05b: THIOGLYCIN (GL3b)
06a: GLYCEROL (GOLa)
06b: GLYCEROL (GOLb)
06c: GLYCEROL (GOLc)
06d: GLYCEROL (GOLd)
06e: GLYCEROL (GOLe)
06f: GLYCEROL (GOLf)
06g: GLYCEROL (GOLg)
06h: GLYCEROL (GOLh)
06i: GLYCEROL (GOLi)
06j: GLYCEROL (GOLj)
06k: GLYCEROL (GOLk)
08a: 2-METHYL-GLUTAMINE (MGNa)
08b: 2-METHYL-GLUTAMINE (MGNb)
07a: MAGNESIUM ION (MGa)
07b: MAGNESIUM ION (MGb)
07c: MAGNESIUM ION (MGc)
07d: MAGNESIUM ION (MGd)
07e: MAGNESIUM ION (MGe)
07f: MAGNESIUM ION (MGf)
07g: MAGNESIUM ION (MGg)
07h: MAGNESIUM ION (MGh)
07i: MAGNESIUM ION (MGi)
07j: MAGNESIUM ION (MGj)
07k: MAGNESIUM ION (MGk)
07l: MAGNESIUM ION (MGl)
07m: MAGNESIUM ION (MGm)
09a: N1-METHYLATED HISTIDINE (MHSa)
09b: N1-METHYLATED HISTIDINE (MHSb)
10a: SODIUM ION (NAa)
10b: SODIUM ION (NAb)
10c: SODIUM ION (NAc)
10d: SODIUM ION (NAd)
10e: SODIUM ION (NAe)
10f: SODIUM ION (NAf)
10g: SODIUM ION (NAg)
10h: SODIUM ION (NAh)
10i: SODIUM ION (NAi)
11a: S-METHYLCYSTEINE (SMCa)
11b: S-METHYLCYSTEINE (SMCb)
12a: COENZYME B (TP7a)
12b: COENZYME B (TP7b)
13a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AGM
2
Mod. Amino Acid
5-METHYL-ARGININE
2
CL
2
Ligand/Ion
CHLORIDE ION
3
COM
2
Ligand/Ion
1-THIOETHANESULFONIC ACID
4
F43
2
Ligand/Ion
FACTOR 430
5
GL3
2
Mod. Amino Acid
THIOGLYCIN
6
GOL
11
Ligand/Ion
GLYCEROL
7
MG
13
Ligand/Ion
MAGNESIUM ION
8
MGN
2
Mod. Amino Acid
2-METHYL-GLUTAMINE
9
MHS
2
Mod. Amino Acid
N1-METHYLATED HISTIDINE
10
NA
9
Ligand/Ion
SODIUM ION
11
SMC
2
Mod. Amino Acid
S-METHYLCYSTEINE
12
TP7
2
Ligand/Ion
COENZYME B
13
ZN
1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(42, 42)
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)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:102 , SER A:215 , ARG A:216 , CYS A:218 , ARG D:102 , SER D:215 , ARG D:216 , CYS D:218
BINDING SITE FOR RESIDUE ZN A 1557
02
AC2
SOFTWARE
GLU A:117 , VAL A:124 , HOH A:2164 , HOH A:2165
BINDING SITE FOR RESIDUE MG A 1558
03
AC3
SOFTWARE
LYS A:11 , PHE A:14 , HOH A:2025 , HOH A:2032 , HOH A:2034 , HOH A:2044
BINDING SITE FOR RESIDUE NA A 1559
04
AC4
SOFTWARE
GOL A:1553 , HOH A:2266 , ARG D:270 , HOH D:2131 , HOH D:2265 , HOH D:2434
BINDING SITE FOR RESIDUE NA A 1560
05
AC5
SOFTWARE
ALA A:544 , THR A:547 , PRO A:548 , HOH A:2427 , HOH A:2428
BINDING SITE FOR RESIDUE NA A 1561
06
AC6
SOFTWARE
PRO A:58 , ILE A:60 , THR A:62 , HOH A:2106 , HOH A:2109 , HOH D:2165
BINDING SITE FOR RESIDUE NA A 1562
07
AC7
SOFTWARE
HOH A:2194 , HOH A:2195
BINDING SITE FOR RESIDUE MG A 1563
08
AC8
SOFTWARE
HOH A:2045 , HOH A:2063
BINDING SITE FOR RESIDUE MG A 1564
09
AC9
SOFTWARE
HOH A:2018 , HOH A:2019 , HOH A:2040 , HOH A:2059
BINDING SITE FOR RESIDUE MG A 1565
10
BC1
SOFTWARE
HOH A:2024 , HOH A:2055 , HOH A:2173 , HOH A:2340
BINDING SITE FOR RESIDUE MG A 1566
11
BC2
SOFTWARE
HOH A:2099 , ASN B:441 , HOH B:2381 , HOH D:2190 , HOH D:2192
BINDING SITE FOR RESIDUE NA B 1445
12
BC3
SOFTWARE
ARG B:235 , HOH B:2116
BINDING SITE FOR RESIDUE CL B 1446
13
BC4
SOFTWARE
ASP B:271 , HOH B:2288 , HOH B:2290 , HOH B:2291 , HOH B:2292
BINDING SITE FOR RESIDUE MG B 1447
14
BC5
SOFTWARE
ASP B:99 , THR B:101 , HOH B:2128 , HOH B:2144 , HOH B:2148 , HOH B:2149
BINDING SITE FOR RESIDUE NA B 1448
15
BC6
SOFTWARE
GLU B:104 , HOH B:2153
BINDING SITE FOR RESIDUE MG B 1449
16
BC7
SOFTWARE
GLU C:30 , HOH C:2027 , HOH C:2053 , HOH C:2056 , HOH C:2144 , HOH F:2046
BINDING SITE FOR RESIDUE MG C 1250
17
BC8
SOFTWARE
GLU D:175 , HOH D:2185 , HOH D:2186 , HOH D:2187
BINDING SITE FOR RESIDUE MG D 1557
18
BC9
SOFTWARE
LYS D:11 , PHE D:14 , HOH D:2011 , HOH D:2017 , HOH D:2020 , HOH D:2025
BINDING SITE FOR RESIDUE NA D 1558
19
CC1
SOFTWARE
ARG A:270 , HOH A:2261 , GOL D:1554 , HOH D:2272 , HOH D:2438
BINDING SITE FOR RESIDUE NA D 1559
20
CC2
SOFTWARE
HOH A:2177 , PRO D:58 , ILE D:60 , THR D:62 , HOH D:2091 , HOH D:2092
BINDING SITE FOR RESIDUE NA D 1560
21
CC3
SOFTWARE
ARG E:235 , HOH E:2104 , HOH E:2301
BINDING SITE FOR RESIDUE CL E 1445
22
CC4
SOFTWARE
ASP E:271 , HOH E:2273 , HOH E:2275 , HOH E:2276
BINDING SITE FOR RESIDUE MG E 1446
23
CC5
SOFTWARE
HOH E:2032 , HOH E:2097 , HOH E:2098
BINDING SITE FOR RESIDUE MG E 1447
24
CC6
SOFTWARE
ASP E:147 , HOH E:2173 , HOH E:2174 , HOH E:2175
BINDING SITE FOR RESIDUE MG E 1448
25
CC7
SOFTWARE
HOH C:2046 , GLU F:30 , HOH F:2052 , HOH F:2055 , HOH F:2146 , HOH F:2151
BINDING SITE FOR RESIDUE MG F 1249
26
CC8
SOFTWARE
GLY A:326 , GLY A:327 , VAL A:328 , GLY A:329 , PHE A:330 , THR A:331 , GLN A:332 , TYR A:333 , PHE A:396 , GLY A:397 , GLY A:442 , PHE A:443 , COM A:1552 , HOH A:2343 , HOH A:2433 , HOH A:2434 , HOH A:2435 , HOH A:2436 , HOH A:2437 , SER B:365 , ILE B:366 , TYR B:367 , LEU C:117 , SER C:118 , GLY C:119 , LYS C:153 , SER C:154 , VAL C:155 , HIS C:156 , HIS C:158 , HOH C:2156 , ALA D:144 , VAL D:145 , VAL D:146 , GLN D:147 , GLN D:230 , MET D:233 , ALA D:243 , HOH D:2241
BINDING SITE FOR RESIDUE F43 A 1550
27
CC9
SOFTWARE
ARG A:270 , LEU A:320 , MET A:324 , PHE A:330 , PHE A:443 , MET A:480 , ASN A:481 , VAL A:482 , HOH A:2295 , HOH A:2438 , HOH A:2439 , HOH A:2440 , PHE B:362 , TYR B:367 , GLY B:368 , GLY B:369 , HIS B:379 , HOH B:2342 , ARG D:225 , LYS D:256 , MHS D:257 , HOH D:2438
BINDING SITE FOR RESIDUE TP7 A 1551
28
DC1
SOFTWARE
TYR A:333 , PHE A:443 , TYR A:444 , F43 A:1550 , HOH A:2441 , PHE B:361 , SER B:365 , TYR B:367 , LEU C:117 , ARG C:120
BINDING SITE FOR RESIDUE COM A 1552
29
DC2
SOFTWARE
ALA A:144 , VAL A:145 , VAL A:146 , GLN A:147 , GLN A:230 , MET A:233 , ALA A:243 , HOH A:2180 , HOH A:2237 , GLY D:326 , GLY D:327 , VAL D:328 , GLY D:329 , PHE D:330 , THR D:331 , GLN D:332 , TYR D:333 , GLY D:397 , GLY D:442 , PHE D:443 , COM D:1552 , HOH D:2427 , HOH D:2428 , HOH D:2429 , HOH D:2430 , SER E:365 , ILE E:366 , TYR E:367 , LEU F:117 , SER F:118 , GLY F:119 , LYS F:153 , SER F:154 , VAL F:155 , HIS F:156 , HIS F:158 , HOH F:2162 , HOH F:2165
BINDING SITE FOR RESIDUE F43 D 1550
30
DC3
SOFTWARE
ARG A:225 , LYS A:256 , MHS A:257 , ARG D:270 , LEU D:320 , MET D:324 , PHE D:330 , PHE D:443 , MET D:480 , ASN D:481 , VAL D:482 , HOH D:2300 , HOH D:2375 , HOH D:2431 , HOH D:2432 , HOH D:2433 , HOH D:2434 , PHE E:362 , TYR E:367 , GLY E:368 , GLY E:369 , HIS E:379 , VAL E:381
BINDING SITE FOR RESIDUE TP7 D 1551
31
DC4
SOFTWARE
TYR D:333 , PHE D:443 , TYR D:444 , F43 D:1550 , HOH D:2435 , PHE E:361 , SER E:365 , TYR E:367 , LEU F:117 , ARG F:120
BINDING SITE FOR RESIDUE COM D 1552
32
DC5
SOFTWARE
SER A:224 , LYS A:256 , HIS A:262 , GLU A:275 , NA A:1560 , HOH A:2266 , HOH D:2265
BINDING SITE FOR RESIDUE GOL A 1553
33
DC6
SOFTWARE
ASP A:170 , ALA A:173 , ASP A:174 , ASP A:183 , ASN A:185 , HOH A:2442 , HOH A:2443
BINDING SITE FOR RESIDUE GOL A 1554
34
DC7
SOFTWARE
VAL A:519 , LYS A:531 , PHE A:537 , GLU A:538 , HOH A:2407 , HOH A:2408
BINDING SITE FOR RESIDUE GOL A 1555
35
DC8
SOFTWARE
LYS A:4 , ASP A:345 , TYR A:348 , GLU A:352 , TYR A:380 , HOH A:2007
BINDING SITE FOR RESIDUE GOL A 1556
36
DC9
SOFTWARE
LYS B:3 , GLU B:25 , SER B:28 , ARG B:31 , GLU B:234 , HOH B:2051 , HOH B:2385 , VAL E:95
BINDING SITE FOR RESIDUE GOL B 1444
37
EC1
SOFTWARE
TYR C:109 , ARG C:110 , ASP C:129 , HOH C:2251 , HOH C:2252 , HOH C:2253 , HOH C:2254
BINDING SITE FOR RESIDUE GOL C 1249
38
EC2
SOFTWARE
ALA D:173 , ASP D:174 , ASP D:183 , ASN D:185 , HOH D:2198 , HOH D:2199 , HOH D:2436 , HOH D:2437
BINDING SITE FOR RESIDUE GOL D 1553
39
EC3
SOFTWARE
SER D:224 , ARG D:225 , LYS D:256 , HIS D:262 , GLU D:275 , NA D:1559 , HOH D:2273 , HOH D:2438
BINDING SITE FOR RESIDUE GOL D 1554
40
EC4
SOFTWARE
GLN D:291 , ARG D:294 , PHE D:513 , ASP D:515 , LEU D:518 , PHE D:520 , ASP D:521 , PHE D:522 , THR D:523 , HOH D:2439
BINDING SITE FOR RESIDUE GOL D 1555
41
EC5
SOFTWARE
ASP D:345 , GLU D:352 , TYR D:380 , HOH D:2001
BINDING SITE FOR RESIDUE GOL D 1556
42
EC6
SOFTWARE
VAL B:95 , LYS E:3 , GLU E:25 , SER E:28 , LEU E:30 , ARG E:31 , GLU E:234 , HOH E:2247
BINDING SITE FOR RESIDUE GOL E 1444
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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[
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
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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
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(5, 10)
Info
All SCOP Domains
1a: SCOP_d1hbua1 (A:270-549)
1b: SCOP_d1hbud1 (D:270-549)
2a: SCOP_d1hbub1 (B:189-443)
2b: SCOP_d1hbue1 (E:189-443)
3a: SCOP_d1hbua2 (A:2-269)
3b: SCOP_d1hbud2 (D:2-269)
4a: SCOP_d1hbub2 (B:2-188)
4b: SCOP_d1hbue2 (E:2-188)
5a: SCOP_d1hbuc_ (C:)
5b: SCOP_d1hbuf_ (F:)
View:
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Families
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Methyl-coenzyme M reductase alpha and beta chain C-terminal domain
(28)
Superfamily
:
Methyl-coenzyme M reductase alpha and beta chain C-terminal domain
(28)
Family
:
Methyl-coenzyme M reductase alpha and beta chain C-terminal domain
(26)
Protein domain
:
Alpha chain
(13)
Methanobacterium thermoautotrophicum [TaxId: 145262]
(11)
1a
d1hbua1
A:270-549
1b
d1hbud1
D:270-549
Protein domain
:
Beta chain
(13)
Methanobacterium thermoautotrophicum [TaxId: 145262]
(11)
2a
d1hbub1
B:189-443
2b
d1hbue1
E:189-443
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
Methyl-coenzyme M reductase subunits
(42)
Family
:
Methyl-coenzyme M reductase alpha and beta chain N-terminal domain
(26)
Protein domain
:
Alpha chain
(13)
Methanobacterium thermoautotrophicum [TaxId: 145262]
(11)
3a
d1hbua2
A:2-269
3b
d1hbud2
D:2-269
Protein domain
:
Beta chain
(13)
Methanobacterium thermoautotrophicum [TaxId: 145262]
(11)
4a
d1hbub2
B:2-188
4b
d1hbue2
E:2-188
Family
:
Methyl-coenzyme M reductase gamma chain
(14)
Protein domain
:
Methyl-coenzyme M reductase gamma chain
(14)
Methanobacterium thermoautotrophicum [TaxId: 145262]
(12)
5a
d1hbuc_
C:
5b
d1hbuf_
F:
[
close SCOP info
]
CATH Domains
(4, 12)
Info
all CATH domains
1a: CATH_1hbuA02 (A:102-276)
1b: CATH_1hbuD02 (D:102-276)
1c: CATH_1hbuB01 (B:45-191)
1d: CATH_1hbuE01 (E:45-191)
2a: CATH_1hbuC00 (C:2-248)
2b: CATH_1hbuF00 (F:2-248)
3a: CATH_1hbuA01 (A:3-101)
3b: CATH_1hbuD01 (D:3-101)
4a: CATH_1hbuA03 (A:277-536)
4b: CATH_1hbuD03 (D:277-536)
4c: CATH_1hbuB02 (B:2-44,B:192-443)
4d: CATH_1hbuE02 (E:2-44,E:192-443)
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Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.470, no name defined]
(7)
Methanothermobacter marburgensis. Organism_taxid: 79929. Strain: marburg.
(1)
1a
1hbuA02
A:102-276
1b
1hbuD02
D:102-276
1c
1hbuB01
B:45-191
1d
1hbuE01
E:45-191
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Lambda Exonuclease; Chain A
(10)
Homologous Superfamily
:
[code=3.90.320.20, no name defined]
(7)
Methanothermobacter marburgensis. Organism_taxid: 79929. Strain: marburg.
(1)
2a
1hbuC00
C:2-248
2b
1hbuF00
F:2-248
Topology
:
Methyl-coenzyme M Reductase; Chain A, domain 1
(7)
Homologous Superfamily
:
Methyl-coenzyme M Reductase; Chain A, domain 1
(7)
Methanothermobacter marburgensis. Organism_taxid: 79929. Strain: marburg.
(1)
3a
1hbuA01
A:3-101
3b
1hbuD01
D:3-101
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Methyl-coenzyme M Reductase; Chain B, domain 2
(7)
Homologous Superfamily
:
Methyl-coenzyme M Reductase; Chain B, domain 2
(7)
Methanothermobacter marburgensis. Organism_taxid: 79929. Strain: marburg.
(1)
4a
1hbuA03
A:277-536
4b
1hbuD03
D:277-536
4c
1hbuB02
B:2-44,B:192-443
4d
1hbuE02
E:2-44,E:192-443
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Atom Selection
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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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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") .
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