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2YP1
Asym. Unit
Info
Asym.Unit (264 KB)
Biol.Unit 1 (130 KB)
Biol.Unit 2 (127 KB)
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(1)
Title
:
CRYSTALLIZATION OF A 45 KDA PEROXYGENASE- PEROXIDASE FROM THE MUSHROOM AGROCYBE AEGERITA AND STRUCTURE DETERMINATION BY SAD UTILIZING ONLY THE HAEM IRON
Authors
:
K. Piontek, E. Strittmatter, R. Ullrich, D. A. Plattner, M. Hofrichter
Date
:
29 Oct 12 (Deposition) - 23 Oct 13 (Release) - 01 Apr 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.31
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,C (1x)
Biol. Unit 2: B,D (1x)
Keywords
:
Oxidoreductase, Peroxidase/Peroxygenase, Unspecific/Aromatic Peroxygenase, Heme, Glycoprotein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Piontek, E. Strittmatter, R. Ullrich, G. Grobe, M. J. Pecyna, M. Kluge, K. Scheibner, M. Hofrichter, D. A. Plattner
Structural Basis Of Substrate Conversion In A New Aromatic Peroxygenase: P450 Functionality With Benefits
J. Biol. Chem. V. 288 34767 2013
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(7, 86)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
1e: ACETATE ION (ACTe)
2a: BETA-D-MANNOSE (BMAa)
2b: BETA-D-MANNOSE (BMAb)
2c: BETA-D-MANNOSE (BMAc)
2d: BETA-D-MANNOSE (BMAd)
2e: BETA-D-MANNOSE (BMAe)
2f: BETA-D-MANNOSE (BMAf)
2g: BETA-D-MANNOSE (BMAg)
3a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
3b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
3c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
3d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
4a: ALPHA-D-MANNOSE (MANa)
4b: ALPHA-D-MANNOSE (MANb)
4c: ALPHA-D-MANNOSE (MANc)
4d: ALPHA-D-MANNOSE (MANd)
4e: ALPHA-D-MANNOSE (MANe)
4f: ALPHA-D-MANNOSE (MANf)
4g: ALPHA-D-MANNOSE (MANg)
4h: ALPHA-D-MANNOSE (MANh)
4i: ALPHA-D-MANNOSE (MANi)
4j: ALPHA-D-MANNOSE (MANj)
4k: ALPHA-D-MANNOSE (MANk)
4l: ALPHA-D-MANNOSE (MANl)
4m: ALPHA-D-MANNOSE (MANm)
4n: ALPHA-D-MANNOSE (MANn)
4o: ALPHA-D-MANNOSE (MANo)
4p: ALPHA-D-MANNOSE (MANp)
4q: ALPHA-D-MANNOSE (MANq)
5a: MAGNESIUM ION (MGa)
5b: MAGNESIUM ION (MGb)
5c: MAGNESIUM ION (MGc)
5d: MAGNESIUM ION (MGd)
6a: N-ACETYL-D-GLUCOSAMINE (NAGa)
6aa: N-ACETYL-D-GLUCOSAMINE (NAGaa)
6ab: N-ACETYL-D-GLUCOSAMINE (NAGab)
6ac: N-ACETYL-D-GLUCOSAMINE (NAGac)
6ad: N-ACETYL-D-GLUCOSAMINE (NAGad)
6ae: N-ACETYL-D-GLUCOSAMINE (NAGae)
6af: N-ACETYL-D-GLUCOSAMINE (NAGaf)
6ag: N-ACETYL-D-GLUCOSAMINE (NAGag)
6ah: N-ACETYL-D-GLUCOSAMINE (NAGah)
6ai: N-ACETYL-D-GLUCOSAMINE (NAGai)
6aj: N-ACETYL-D-GLUCOSAMINE (NAGaj)
6b: N-ACETYL-D-GLUCOSAMINE (NAGb)
6c: N-ACETYL-D-GLUCOSAMINE (NAGc)
6d: N-ACETYL-D-GLUCOSAMINE (NAGd)
6e: N-ACETYL-D-GLUCOSAMINE (NAGe)
6f: N-ACETYL-D-GLUCOSAMINE (NAGf)
6g: N-ACETYL-D-GLUCOSAMINE (NAGg)
6h: N-ACETYL-D-GLUCOSAMINE (NAGh)
6i: N-ACETYL-D-GLUCOSAMINE (NAGi)
6j: N-ACETYL-D-GLUCOSAMINE (NAGj)
6k: N-ACETYL-D-GLUCOSAMINE (NAGk)
6l: N-ACETYL-D-GLUCOSAMINE (NAGl)
6m: N-ACETYL-D-GLUCOSAMINE (NAGm)
6n: N-ACETYL-D-GLUCOSAMINE (NAGn)
6o: N-ACETYL-D-GLUCOSAMINE (NAGo)
6p: N-ACETYL-D-GLUCOSAMINE (NAGp)
6q: N-ACETYL-D-GLUCOSAMINE (NAGq)
6r: N-ACETYL-D-GLUCOSAMINE (NAGr)
6s: N-ACETYL-D-GLUCOSAMINE (NAGs)
6t: N-ACETYL-D-GLUCOSAMINE (NAGt)
6u: N-ACETYL-D-GLUCOSAMINE (NAGu)
6v: N-ACETYL-D-GLUCOSAMINE (NAGv)
6w: N-ACETYL-D-GLUCOSAMINE (NAGw)
6x: N-ACETYL-D-GLUCOSAMINE (NAGx)
6y: N-ACETYL-D-GLUCOSAMINE (NAGy)
6z: N-ACETYL-D-GLUCOSAMINE (NAGz)
7a: SULFATE ION (SO4a)
7b: SULFATE ION (SO4b)
7c: SULFATE ION (SO4c)
7d: SULFATE ION (SO4d)
7e: SULFATE ION (SO4e)
7f: SULFATE ION (SO4f)
7g: SULFATE ION (SO4g)
7h: SULFATE ION (SO4h)
7i: SULFATE ION (SO4i)
7j: SULFATE ION (SO4j)
7k: SULFATE ION (SO4k)
7l: SULFATE ION (SO4l)
7m: SULFATE ION (SO4m)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
5
Ligand/Ion
ACETATE ION
2
BMA
7
Ligand/Ion
BETA-D-MANNOSE
3
HEM
4
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
4
MAN
17
Ligand/Ion
ALPHA-D-MANNOSE
5
MG
4
Ligand/Ion
MAGNESIUM ION
6
NAG
36
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
7
SO4
13
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(46, 46)
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)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
45: EC9 (SOFTWARE)
46: FC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PRO A:35 , CYS A:36 , PRO A:37 , LEU A:39 , VAL A:63 , PHE A:69 , ALA A:77 , THR A:78 , ALA A:81 , PHE A:121 , GLU A:122 , GLY A:123 , SER A:126 , MET A:127 , THR A:128 , ARG A:189 , GLU A:196 , PHE A:199 , PHE A:204 , MG A:353 , ACT A:1327 , HOH A:2041 , HOH A:2123 , HOH A:2159
BINDING SITE FOR RESIDUE HEM A 350
02
AC2
SOFTWARE
GLU A:122 , GLY A:123 , SER A:126 , HEM A:350 , HOH A:2123 , HOH A:2124
BINDING SITE FOR RESIDUE MG A 353
03
AC3
SOFTWARE
ALA A:77 , GLU A:196 , PHE A:199 , HEM A:350 , HOH A:2323
BINDING SITE FOR RESIDUE ACT A1327
04
AC4
SOFTWARE
CYS B:36 , PRO B:37 , GLY B:38 , VAL B:63 , PHE B:69 , ALA B:77 , THR B:78 , PHE B:121 , GLU B:122 , GLY B:123 , SER B:126 , MET B:127 , THR B:128 , ARG B:189 , GLU B:196 , PHE B:199 , LEU B:203 , MG B:353 , ACT B:1328 , HOH B:2157 , HOH B:2199
BINDING SITE FOR RESIDUE HEM B 350
05
AC5
SOFTWARE
GLU B:122 , GLY B:123 , SER B:126 , HEM B:350 , HOH B:2157 , HOH B:2158
BINDING SITE FOR RESIDUE MG B 353
06
AC6
SOFTWARE
GLU B:196 , PHE B:199 , HEM B:350 , HOH B:2368
BINDING SITE FOR RESIDUE ACT B1328
07
AC7
SOFTWARE
PRO C:35 , CYS C:36 , PRO C:37 , GLY C:38 , PHE C:69 , ALA C:77 , THR C:78 , ALA C:81 , PHE C:121 , GLU C:122 , GLY C:123 , SER C:126 , MET C:127 , THR C:128 , ARG C:189 , GLU C:196 , PHE C:199 , LEU C:203 , MG C:353 , ACT C:1329 , HOH C:2131
BINDING SITE FOR RESIDUE HEM C 350
08
AC8
SOFTWARE
GLU C:122 , GLY C:123 , SER C:126 , HEM C:350 , HOH C:2131 , HOH C:2132
BINDING SITE FOR RESIDUE MG C 353
09
AC9
SOFTWARE
ALA C:77 , PHE C:121 , THR C:192 , GLU C:196 , PHE C:199 , HEM C:350
BINDING SITE FOR RESIDUE ACT C1329
10
BC1
SOFTWARE
CYS D:36 , PRO D:37 , GLY D:38 , LEU D:39 , PHE D:69 , ALA D:77 , THR D:78 , ALA D:81 , PHE D:121 , GLU D:122 , GLY D:123 , SER D:126 , MET D:127 , THR D:128 , ARG D:189 , GLU D:196 , PHE D:199 , LEU D:203 , MG D:353 , ACT D:1327 , HOH D:2029 , HOH D:2083 , HOH D:2104
BINDING SITE FOR RESIDUE HEM D 350
11
BC2
SOFTWARE
GLU D:122 , GLY D:123 , SER D:126 , HEM D:350 , HOH D:2083 , HOH D:2084
BINDING SITE FOR RESIDUE MG D 353
12
BC3
SOFTWARE
ALA D:77 , GLU D:196 , PHE D:199 , HEM D:350 , HOH D:2193
BINDING SITE FOR RESIDUE ACT D1327
13
BC4
SOFTWARE
ARG C:97 , THR C:99 , ARG C:100 , HOH C:2092 , HOH C:2094
BINDING SITE FOR RESIDUE SO4 C1330
14
BC5
SOFTWARE
ARG A:97 , THR A:99 , ARG A:100 , HOH A:2034 , HOH A:2096
BINDING SITE FOR RESIDUE SO4 A1328
15
BC6
SOFTWARE
ARG B:97 , THR B:99 , ARG B:100
BINDING SITE FOR RESIDUE SO4 B1329
16
BC7
SOFTWARE
ARG C:97 , HIS C:138 , HOH C:2039 , HOH C:2290
BINDING SITE FOR RESIDUE SO4 C1331
17
BC8
SOFTWARE
ARG A:97 , HOH A:2035 , HOH A:2039 , HOH A:2324 , HOH A:2325
BINDING SITE FOR RESIDUE SO4 A1329
18
BC9
SOFTWARE
TYR A:151 , ARG A:154 , LYS A:171
BINDING SITE FOR RESIDUE SO4 A1330
19
CC1
SOFTWARE
ARG B:97 , HIS B:138 , HOH B:2369
BINDING SITE FOR RESIDUE SO4 B1330
20
CC2
SOFTWARE
THR D:99 , ARG D:100 , HOH D:2064 , HOH D:2194 , HOH D:2195
BINDING SITE FOR RESIDUE SO4 D1328
21
CC3
SOFTWARE
THR A:163 , NAG A:371 , NAG A:372 , HOH A:2156 , THR C:276 , PRO C:277 , CYS C:278 , LEU C:279
BINDING SITE FOR RESIDUE SO4 C1332
22
CC4
SOFTWARE
THR B:163 , NAG B:371 , NAG B:372 , HOH B:2196 , HOH B:2351 , THR D:276 , PRO D:277 , CYS D:278 , LEU D:279
BINDING SITE FOR RESIDUE SO4 D1329
23
CC5
SOFTWARE
ASN C:141 , GLU C:142 , THR C:143 , NAG C:361 , HOH C:2148 , HOH C:2291
BINDING SITE FOR RESIDUE SO4 C1333
24
CC6
SOFTWARE
THR B:276 , PRO B:277 , CYS B:278 , LEU B:279 , HOH B:2289 , THR D:163 , NAG D:371 , NAG D:372
BINDING SITE FOR RESIDUE SO4 B1331
25
CC7
SOFTWARE
ASN B:51 , VAL B:53 , HOH B:2125 , ARG C:100 , LEU C:101 , GLY C:103
BINDING SITE FOR RESIDUE ACT C1334
26
CC8
SOFTWARE
THR A:276 , PRO A:277 , CYS A:278 , LEU A:279 , HOH A:2258 , HOH A:2326 , THR C:163 , NAG C:371 , NAG C:372
BINDING SITE FOR RESIDUE SO4 A1331
27
CC9
SOFTWARE
ASN A:11 , SER A:13 , LYS A:15 , HOH A:2012 , HOH A:2321 , HOH A:2322 , GLU C:10
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 11 RESIDUES 411 TO 412
28
DC1
SOFTWARE
PHE A:133 , PHE A:134 , ASN A:141 , THR A:179 , PRO A:181 , HOH A:2131 , HOH A:2302 , HOH A:2304 , HOH A:2307
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 141 RESIDUES 361 TO 366
29
DC2
SOFTWARE
PHE A:155 , GLY A:156 , GLY A:157 , ASN A:161 , THR A:163 , GLN A:213 , HOH A:2308 , CYS C:278 , LEU C:279 , GLU C:282 , ALA C:317 , CYS C:319 , SO4 C:1332
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 161 RESIDUES 371 TO 375
30
DC3
SOFTWARE
PHE A:133 , ASN A:182 , HOH A:2311 , THR D:266 , VAL D:267 , HOH D:2147
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 182 RESIDUES 381 TO 382
31
DC4
SOFTWARE
ASN A:286 , LYS A:290 , PRO A:324 , GLY A:326 , HOH A:2262 , HOH A:2301 , HOH A:2313 , HOH A:2314 , HOH A:2315 , HOH A:2317 , HOH A:2318 , HOH A:2319 , HOH A:2320 , GLU D:142 , PHE D:145 , GLU D:146 , VAL D:149 , ASP D:150 , ASN D:153 , ARG D:154 , MET D:216 , ASP D:217 , ARG D:220
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 286 RESIDUES 391 TO 398
32
DC5
SOFTWARE
ASN B:11 , ALA B:14 , HOH B:2366
BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 11 RESIDUES 411 TO 412
33
DC6
SOFTWARE
PHE B:133 , PHE B:134 , ASN B:141 , LEU B:144 , THR B:179 , HOH B:2168 , HOH B:2175 , HOH B:2346 , HOH B:2347 , HOH B:2348 , HOH B:2349
BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 141 RESIDUES 361 TO 365
34
DC7
SOFTWARE
PHE B:155 , GLY B:156 , GLY B:157 , ASN B:161 , THR B:163 , GLN B:213 , HOH B:2190 , HOH B:2191 , HOH B:2236 , HOH B:2350 , HOH B:2351 , CYS D:278 , GLU D:282 , ALA D:317 , CYS D:319 , SO4 D:1329
BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 161 RESIDUES 371 TO 372
35
DC8
SOFTWARE
PHE B:133 , ASN B:182 , HOH B:2166 , HOH B:2352 , HOH B:2355 , HOH B:2356
BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 182 RESIDUES 381 TO 382
36
DC9
SOFTWARE
ASN B:286 , LYS B:290 , PRO B:324 , GLY B:326 , HOH B:2295 , HOH B:2341 , HOH B:2342 , HOH B:2357 , HOH B:2358 , HOH B:2359 , HOH B:2360 , HOH B:2361 , HOH B:2362 , HOH B:2363 , HOH B:2364 , HOH B:2365 , GLU C:142 , GLU C:146 , VAL C:149 , ASP C:150 , ASN C:153 , MET C:216 , ASP C:217 , ARG C:220
BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 286 RESIDUES 391 TO 398
37
EC1
SOFTWARE
ASN C:11 , ALA C:14 , HOH C:2288
BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 11 RESIDUES 411 TO 412
38
EC2
SOFTWARE
ASN C:141 , SO4 C:1333 , HOH C:2284
BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 141 RESIDUES 361 TO 363
39
EC3
SOFTWARE
CYS A:278 , GLU A:282 , ALA A:317 , CYS A:319 , SO4 A:1331 , HOH A:2294 , PHE C:155 , GLY C:156 , GLY C:157 , ASN C:161 , THR C:163 , GLN C:213 , HOH C:2153
BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 161 RESIDUES 371 TO 372
40
EC4
SOFTWARE
PHE C:133 , ASN C:182 , HOH C:2286
BINDING SITE FOR MONO-SACCHARIDE NAG C 381 BOUND TO ASN C 182
41
EC5
SOFTWARE
ASN C:286 , LYS C:290 , PHE C:323 , PRO C:324 , HOH C:2237 , HOH C:2240 , HOH C:2280 , HOH C:2287
BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 286 RESIDUES 391 TO 392
42
EC6
SOFTWARE
GLU B:10 , ASN D:11 , SER D:13 , ALA D:14 , LYS D:15
BINDING SITE FOR MONO-SACCHARIDE NAG D 411 BOUND TO ASN D 11
43
EC7
SOFTWARE
ASN D:141 , HOH D:2190
BINDING SITE FOR CHAIN D OF SUGAR BOUND TO ASN D 141 RESIDUES 361 TO 362
44
EC8
SOFTWARE
CYS B:278 , GLU B:282 , ALA B:317 , CYS B:319 , SO4 B:1331 , HOH B:2335 , PHE D:155 , GLY D:156 , ASN D:161 , THR D:163 , GLN D:213 , HOH D:2098
BINDING SITE FOR CHAIN D OF SUGAR BOUND TO ASN D 161 RESIDUES 371 TO 373
45
EC9
SOFTWARE
ASN D:182
BINDING SITE FOR MONO-SACCHARIDE NAG D 381 BOUND TO ASN D 182
46
FC1
SOFTWARE
ASN D:286 , LYS D:290 , PHE D:323 , PRO D:324 , HOH D:2189
BINDING SITE FOR MONO-SACCHARIDE NAG D 391 BOUND TO ASN D 286
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: HEME_HALOPEROXIDASE (A:20-248,B:20-248,C:20-248,D:20-24...)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
HEME_HALOPEROXIDASE
PS51405
Heme haloperoxidase family profile.
APO1_AGRAE
63-291
4
A:20-248
B:20-248
C:20-248
D:20-248
[
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
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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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Atom Selection
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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
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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Asym.Unit (264 KB)
Header - Asym.Unit
Biol.Unit 1 (130 KB)
Header - Biol.Unit 1
Biol.Unit 2 (127 KB)
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