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3WG7
Biol. Unit 1
Info
Asym.Unit (700 KB)
Biol.Unit 1 (346 KB)
Biol.Unit 2 (341 KB)
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Title
:
A 1.9 ANGSTROM RADIATION DAMAGE FREE X-RAY STRUCTURE OF LARGE (420KDA) PROTEIN BY FEMTOSECOND CRYSTALLOGRAPHY
Authors
:
K. Hirata, K. Shinzawa-Itoh, N. Yano, S. Takemura, K. Kato, M. Hatanaka K. Muramoto, T. Kawahara, T. Tsukihara, E. Yamashita, K. Tono, G. Ueno T. Hikima, H. Murakami, Y. Inubushi, M. Yabashi, T. Ishikawa, M. Yamam T. Ogura, H. Sugimoto, J. R. Shen, S. Yoshikawa, H. Ago
Date
:
29 Jul 13 (Deposition) - 30 Apr 14 (Release) - 25 Jun 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L,M (1x)
Biol. Unit 2: N,O,P,Q,R,S,T,U,V,W,X,Y,Z (1x)
Keywords
:
Electron Transport Complex Iv, Iron, Oxidation-Reduction, Protein Interaction Domains, Motifs, Oxidoreductase, Membrane
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Hirata, K. Shinzawa-Itoh, N. Yano, S. Takemura, K. Kato, M. Hatanaka, K. Muramoto, T. Kawahara, T. Tsukihara, E. Yamashita, K. Tono, G. Ueno, T. Hikima, H. Murakami, Y. Inubushi, M. Yabashi, T. Ishikawa, M. Yamamoto, T. Ogura, H. Sugimoto, J. R. Shen, S. Yoshikawa, H. Ago
Determination Of Damage-Free Crystal Structure Of An X-Ray-Sensitive Protein Using An Xfel.
Nat. Methods 2014
[
close entry info
]
Hetero Components
(13, 27)
Info
All Hetero Components
01a: CARDIOLIPIN (CDLa)
01b: CARDIOLIPIN (CDLb)
01c: CARDIOLIPIN (CDLc)
01d: CARDIOLIPIN (CDLd)
02a: CHOLIC ACID (CHDa)
02b: CHOLIC ACID (CHDb)
02c: CHOLIC ACID (CHDc)
02d: CHOLIC ACID (CHDd)
02e: CHOLIC ACID (CHDe)
02f: CHOLIC ACID (CHDf)
02g: CHOLIC ACID (CHDg)
02h: CHOLIC ACID (CHDh)
04a: DINUCLEAR COPPER ION (CUAa)
04b: DINUCLEAR COPPER ION (CUAb)
03a: COPPER (II) ION (CUa)
04b: COPPER (II) ION (CUb)
05a: DECYL-BETA-D-MALTOPYRANOSIDE (DMUa)
05b: DECYL-BETA-D-MALTOPYRANOSIDE (DMUb)
06a: N-FORMYLMETHIONINE (FMEa)
06b: N-FORMYLMETHIONINE (FMEb)
06c: N-FORMYLMETHIONINE (FMEc)
06d: N-FORMYLMETHIONINE (FMEd)
07a: HEME-A (HEAa)
07b: HEME-A (HEAb)
07c: HEME-A (HEAc)
07d: HEME-A (HEAd)
08a: MAGNESIUM ION (MGa)
08b: MAGNESIUM ION (MGb)
09a: SODIUM ION (NAa)
09b: SODIUM ION (NAb)
09c: SODIUM ION (NAc)
09d: SODIUM ION (NAd)
10a: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)P... (PEKa)
10b: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)P... (PEKb)
10c: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)P... (PEKc)
10d: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)P... (PEKd)
10e: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)P... (PEKe)
10f: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)P... (PEKf)
11a: PEROXIDE ION (PERa)
11b: PEROXIDE ION (PERb)
12a: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVa)
12b: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVb)
12c: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVc)
12d: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVd)
12e: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVe)
12f: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVf)
12g: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVg)
12h: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVh)
13a: (7R,17E,20E)-4-HYDROXY-N,N,N-TRIME... (PSCa)
13b: (7R,17E,20E)-4-HYDROXY-N,N,N-TRIME... (PSCb)
14a: N-ACETYL-SERINE (SACa)
14b: N-ACETYL-SERINE (SACb)
15a: TRISTEAROYLGLYCEROL (TGLa)
15b: TRISTEAROYLGLYCEROL (TGLb)
15c: TRISTEAROYLGLYCEROL (TGLc)
15d: TRISTEAROYLGLYCEROL (TGLd)
15e: TRISTEAROYLGLYCEROL (TGLe)
15f: TRISTEAROYLGLYCEROL (TGLf)
16a: PHOSPHOTHREONINE (TPOa)
16b: PHOSPHOTHREONINE (TPOb)
17a: ZINC ION (ZNa)
17b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CDL
2
Ligand/Ion
CARDIOLIPIN
2
CHD
5
Ligand/Ion
CHOLIC ACID
3
CU
-1
Ligand/Ion
COPPER (II) ION
4
CUA
1
Ligand/Ion
DINUCLEAR COPPER ION
5
DMU
1
Ligand/Ion
DECYL-BETA-D-MALTOPYRANOSIDE
6
FME
2
Mod. Amino Acid
N-FORMYLMETHIONINE
7
HEA
2
Ligand/Ion
HEME-A
8
MG
-1
Ligand/Ion
MAGNESIUM ION
9
NA
-1
Ligand/Ion
SODIUM ION
10
PEK
3
Ligand/Ion
(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE
11
PER
1
Ligand/Ion
PEROXIDE ION
12
PGV
4
Ligand/Ion
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
13
PSC
1
Ligand/Ion
(7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE
14
SAC
1
Mod. Amino Acid
N-ACETYL-SERINE
15
TGL
3
Ligand/Ion
TRISTEAROYLGLYCEROL
16
TPO
1
Mod. Amino Acid
PHOSPHOTHREONINE
17
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(33, 33)
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: EC4 (SOFTWARE)
30: FC1 (SOFTWARE)
31: FC2 (SOFTWARE)
32: FC5 (SOFTWARE)
33: FC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
MET A:28 , THR A:31 , SER A:34 , ILE A:37 , ARG A:38 , TYR A:54 , VAL A:58 , HIS A:61 , ALA A:62 , MET A:65 , ILE A:66 , VAL A:70 , ILE A:73 , GLY A:125 , TRP A:126 , TYR A:371 , PHE A:377 , HIS A:378 , SER A:382 , VAL A:386 , MET A:390 , PHE A:393 , MET A:417 , PHE A:425 , GLN A:428 , ARG A:438 , ARG A:439 , TYR A:440 , SER A:458 , VAL A:465 , MET A:468 , HOH A:704 , HOH A:725 , HOH A:732
BINDING SITE FOR RESIDUE HEA A 601
02
AC2
SOFTWARE
TRP A:126 , TRP A:236 , VAL A:243 , TYR A:244 , HIS A:290 , HIS A:291 , THR A:309 , ILE A:312 , THR A:316 , GLY A:317 , GLY A:352 , GLY A:355 , ILE A:356 , LEU A:358 , ALA A:359 , ASP A:364 , HIS A:368 , VAL A:373 , HIS A:376 , PHE A:377 , VAL A:380 , LEU A:381 , ARG A:438 , PER A:606 , HOH A:705 , HOH A:712 , HOH A:723 , HOH A:731 , ILE B:34
BINDING SITE FOR RESIDUE HEA A 602
03
AC3
SOFTWARE
HIS A:240 , HIS A:290 , HIS A:291 , PER A:606
BINDING SITE FOR RESIDUE CU A 603
04
AC4
SOFTWARE
HIS A:368 , ASP A:369 , HOH A:722 , GLU B:198 , HOH B:410 , HOH B:411
BINDING SITE FOR RESIDUE MG A 604
05
AC5
SOFTWARE
GLU A:40 , GLY A:45 , SER A:441 , HOH A:720
BINDING SITE FOR RESIDUE NA A 605
06
AC6
SOFTWARE
HIS A:240 , VAL A:243 , HIS A:291 , HEA A:602 , CU A:603
BINDING SITE FOR RESIDUE PER A 606
07
AC7
SOFTWARE
PHE A:94 , PRO A:95 , ARG A:96 , MET A:97 , HOH A:776 , HIS C:9 , ALA C:24 , ASN C:50 , TRP C:57 , TRP C:58 , GLU C:64 , HIS C:71 , LEU C:79 , GLY C:82 , PEK C:302 , PGV C:303
BINDING SITE FOR RESIDUE PGV A 607
08
AC8
SOFTWARE
ASN A:406 , THR A:408 , HOH A:778 , HOH A:931 , PHE D:87 , PHE K:9 , HIS K:10 , PRO M:12 , LEU M:19 , HOH M:2316
BINDING SITE FOR RESIDUE PGV A 608
09
AC9
SOFTWARE
ASN A:422 , PHE A:426 , PHE A:430 , LEU A:433 , LEU B:7 , LEU B:28 , PHE B:32 , SER B:35 , LEU B:39
BINDING SITE FOR RESIDUE TGL B 301
10
BC1
SOFTWARE
HIS B:161 , CYS B:196 , GLU B:198 , CYS B:200 , HIS B:204 , MET B:207
BINDING SITE FOR RESIDUE CUA B 302
11
BC2
SOFTWARE
MET A:271 , TRP A:275 , GLN B:59 , GLU B:62 , THR B:63 , THR B:66 , HOH B:455 , HOH B:508 , PEK P:308 , ARG T:14 , ARG T:17 , PHE T:21 , GLY T:22
BINDING SITE FOR RESIDUE CHD B 303
12
BC3
SOFTWARE
PHE A:321 , ILE B:41 , HIS B:52 , MET B:56 , ASP B:57 , GLU B:60 , HOH B:576 , HIS E:5 , ASP E:8 , PHE E:11 , LEU E:41 , HOH E:217 , ARG I:10
BINDING SITE FOR RESIDUE PSC B 304
13
BC4
SOFTWARE
HIS C:148 , HIS C:232 , GLU C:236 , HOH C:404
BINDING SITE FOR RESIDUE NA C 301
14
BC5
SOFTWARE
VAL A:155 , ALA A:203 , PGV A:607 , TYR C:181 , TYR C:182 , ALA C:184 , PHE C:186 , THR C:187 , ILE C:188 , PHE C:198 , GLY C:202 , PHE C:203 , TRP G:62 , THR G:68 , PHE G:69 , PHE G:70 , HIS G:71 , ASN G:76 , HOH G:205
BINDING SITE FOR RESIDUE PEK C 302
15
BC6
SOFTWARE
PGV A:607 , MET C:54 , VAL C:61 , SER C:65 , THR C:66 , ILE C:210 , PHE C:214 , ARG C:221 , HIS C:226 , PHE C:227 , HIS C:231 , PHE C:233 , GLY C:234 , CDL C:304 , HOH C:432 , HOH C:447 , HOH C:475 , HOH F:207
BINDING SITE FOR RESIDUE PGV C 303
16
BC7
SOFTWARE
THR C:48 , MET C:51 , LEU C:52 , MET C:54 , TYR C:55 , TRP C:58 , ARG C:59 , ILE C:62 , ARG C:63 , PHE C:67 , SER C:212 , THR C:213 , ILE C:216 , PHE C:220 , ARG C:221 , LYS C:224 , HIS C:226 , PGV C:303 , HOH C:421 , HOH C:500 , HOH C:513 , HOH C:537 , LYS J:8 , LEU J:31
BINDING SITE FOR RESIDUE CDL C 304
17
BC8
SOFTWARE
ARG C:156 , PHE C:164 , PHE C:219 , LEU C:223 , HOH C:510 , PHE J:1
BINDING SITE FOR RESIDUE CHD C 305
18
BC9
SOFTWARE
HIS A:233 , ASP A:300 , THR A:301 , TYR A:304 , TRP C:99 , HIS C:103 , PGV C:308 , HOH C:503 , HOH C:535 , LEU P:127
BINDING SITE FOR RESIDUE CHD C 306
19
CC1
SOFTWARE
LYS C:157 , HIS C:158 , GLN C:161 , HOH C:525 , ARG G:17 , GLY G:22 , CDL G:101 , CHD G:103 , HOH G:231 , SER N:279 , ILE N:311 , GLN O:59 , HOH O:486
BINDING SITE FOR RESIDUE PEK C 307
20
CC2
SOFTWARE
PHE A:237 , THR C:95 , TRP C:99 , TYR C:102 , HIS C:103 , ALA C:107 , CHD C:306 , HOH C:523 , HOH C:538 , ASN H:24 , ALA T:1
BINDING SITE FOR RESIDUE PGV C 308
21
CC3
SOFTWARE
TRP A:334 , LEU A:342 , GLY A:343 , ALA A:415 , PHE A:418 , VAL A:419 , HOH A:908 , LEU B:46 , THR B:47 , LYS B:49 , HOH B:452 , ARG D:73 , SER D:74 , THR D:75 , GLU D:77 , TRP D:78 , HOH D:401 , ARG I:16 , HIS I:20
BINDING SITE FOR RESIDUE TGL D 201
22
CC4
SOFTWARE
CYS F:60 , CYS F:62 , CYS F:82 , CYS F:85
BINDING SITE FOR RESIDUE ZN F 101
23
CC5
SOFTWARE
LEU C:127 , LEU C:131 , LEU C:138 , VAL C:254 , PEK C:307 , HOH C:528 , SER G:27 , LEU G:30 , ASN G:34 , LEU G:37 , HIS G:38 , HOH G:231 , HOH G:241 , HOH G:265 , PHE N:282 , ILE N:286 , ASP N:300 , SER N:307 , ILE N:311 , ILE N:314 , ALA O:70 , LEU O:78 , LEU O:81 , TYR O:85
BINDING SITE FOR RESIDUE CDL G 101
24
CC6
SOFTWARE
SER G:2 , LYS G:5 , GLY G:6 , HOH G:236 , HOH G:266 , LYS P:77 , ARG P:80 , TYR P:81 , VAL P:91 , THR P:95 , PHE P:98 , TRP P:240 , VAL P:247
BINDING SITE FOR RESIDUE PEK G 102
25
CC7
SOFTWARE
PEK C:307 , ARG G:14 , ARG G:17 , PHE G:21 , GLY G:22 , HOH G:211 , HOH G:228 , HOH G:263 , MET N:271 , TRP N:275 , GLU O:62 , THR O:63
BINDING SITE FOR RESIDUE CHD G 103
26
CC8
SOFTWARE
ILE A:3 , TYR J:32 , ARG J:33 , MET J:36 , THR J:37
BINDING SITE FOR RESIDUE CHD J 101
27
CC9
SOFTWARE
THR A:17 , PHE A:22 , TRP A:25 , PHE A:400 , SER A:401 , PRO L:12 , PHE L:13 , SER L:14 , ARG L:20 , MET L:24 , PHE L:28 , PHE L:29 , SER L:31
BINDING SITE FOR RESIDUE TGL L 101
28
DC1
SOFTWARE
TRP D:98 , LEU M:28 , TRP M:32 , TYR M:35 , HIS M:36 , HOH M:2331
BINDING SITE FOR RESIDUE DMU M 101
29
EC4
SOFTWARE
ALA G:1 , HOH N:956 , TYR P:102 , HIS P:103 , ALA P:107 , CHD P:307 , HOH P:512 , ASN U:24 , HOH U:123
BINDING SITE FOR RESIDUE PGV P 301
30
FC1
SOFTWARE
LEU C:127 , HIS N:233 , ASP N:300 , THR N:301 , TYR N:304 , TRP P:99 , HIS P:103 , PGV P:301 , HOH P:492
BINDING SITE FOR RESIDUE CHD P 307
31
FC2
SOFTWARE
SER A:279 , ILE A:311 , CHD B:303 , HOH B:582 , LYS P:157 , HIS P:158 , GLN P:161 , THR P:168 , TYR P:172 , HOH P:530 , HOH P:539 , ALA S:1 , ARG T:17 , GLY T:22 , LEU T:25 , CDL T:102
BINDING SITE FOR RESIDUE PEK P 308
32
FC5
SOFTWARE
LYS C:77 , ARG C:80 , TYR C:81 , ILE C:84 , PHE C:98 , TRP C:240 , HOH C:529 , HOH C:536 , SER T:2 , ALA T:3 , LYS T:5 , GLY T:6 , HIS T:8 , CDL T:102
BINDING SITE FOR RESIDUE PEK T 101
33
FC6
SOFTWARE
ASP A:300 , ALA A:303 , SER A:307 , ALA A:308 , ILE A:311 , ILE A:314 , LEU B:81 , ARG B:82 , TYR B:85 , LEU P:127 , LEU P:131 , PEK P:308 , HOH P:515 , HOH P:529 , SER T:27 , LEU T:30 , CYS T:31 , ASN T:34 , LEU T:37 , HIS T:38 , PEK T:101 , HOH T:222 , HOH T:238
BINDING SITE FOR RESIDUE CDL T 102
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(10, 10)
Info
All PROSITE Patterns/Profiles
01: COX2_TM (B:1-91)
02: COX1 (A:1-514)
03: COX3 (C:4-261)
04: CHCH (H:26-72)
05: COX5B_2 (F:1-98)
06: COX6A (G:55-72)
07: COX2_CUA (B:92-225)
08: COX5B_1 (F:69-91)
09: COX2 (B:159-207)
10: COX1_CUB (A:236-291)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
COX2_TM
PS50999
Cytochrome oxidase subunit II transmembrane region profile.
COX2_BOVIN
1-91
1
B:1-91
-
2
COX1
PS50855
Cytochrome oxidase subunit I profile.
COX1_BOVIN
1-514
1
A:1-514
-
3
COX3
PS50253
Heme-copper oxidase subunit III family profile.
COX3_BOVIN
4-261
1
C:4-261
-
4
CHCH
PS51808
Coiled coil-helix-coiled coil-helix (CHCH) domain profile.
CX6B1_BOVIN
27-73
1
H:26-72
-
5
COX5B_2
PS51359
Cytochrome c oxidase subunit Vb, zinc binding domain profile.
COX5B_BOVIN
32-129
1
F:1-98
-
6
COX6A
PS01329
Cytochrome c oxidase subunit VIa signature.
CX6A2_BOVIN
67-84
1
G:55-72
-
7
COX2_CUA
PS50857
Cytochrome oxidase subunit II copper A binding domain profile.
COX2_BOVIN
92-225
1
B:92-225
-
8
COX5B_1
PS00848
Cytochrome c oxidase subunit Vb, zinc binding region signature.
COX5B_BOVIN
100-122
1
F:69-91
-
9
COX2
PS00078
CO II and nitrous oxide reductase dinuclear copper centers signature.
COX2_BOVIN
159-207
1
B:159-207
-
10
COX1_CUB
PS00077
Heme-copper oxidase catalytic subunit, copper B binding region signature.
COX1_BOVIN
236-291
1
A:236-291
-
[
close PROSITE info
]
Exons
(0, 0)
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All Exons
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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
(0, 0)
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CATH Domains
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all CATH domains
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Pfam Domains
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all PFAM domains
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Asymmetric Unit 1
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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
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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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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") .
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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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