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3S4T
Asym. Unit
Info
Asym.Unit (921 KB)
Biol.Unit 1 (456 KB)
Biol.Unit 2 (234 KB)
Biol.Unit 3 (232 KB)
Biol.Unit 4 (458 KB)
Biol.Unit 5 (232 KB)
Biol.Unit 6 (234 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF PUTATIVE AMIDOHYDROLASE-2 (EFI-TARGET 500288)FROM POLAROMONAS SP. JS666
Authors
:
U. A. Ramagopal, R. Toro, J. A. Girlt, S. C. Almo, Enzyme Function Init
Date
:
20 May 11 (Deposition) - 24 Aug 11 (Release) - 24 Aug 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: A,B (1x)
Biol. Unit 3: C,D (1x)
Biol. Unit 4: E,F,G,H (1x)
Biol. Unit 5: E,F (1x)
Biol. Unit 6: G,H (1x)
Keywords
:
Enzyme Function Initiative, Efi, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
U. A. Ramagopal, R. Toro, J. A. Girlt, S. C. Almo
Crystal Structure Of Putative Amidohydrolase-2 (Efi-Target 500288)From Polaromonas Sp. Js666
To Be Published
[
close entry info
]
Hetero Components
(6, 129)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
1e: ACETATE ION (ACTe)
1f: ACETATE ION (ACTf)
1g: ACETATE ION (ACTg)
1h: ACETATE ION (ACTh)
1i: ACETATE ION (ACTi)
1j: ACETATE ION (ACTj)
1k: ACETATE ION (ACTk)
1l: ACETATE ION (ACTl)
1m: ACETATE ION (ACTm)
1n: ACETATE ION (ACTn)
1o: ACETATE ION (ACTo)
1p: ACETATE ION (ACTp)
2a: CHLORIDE ION (CLa)
3a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
3b: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEb)
3c: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEc)
3d: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEd)
3e: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEe)
3f: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEf)
3g: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEg)
4a: GLYCEROL (GOLa)
4b: GLYCEROL (GOLb)
4c: GLYCEROL (GOLc)
5a: SELENOMETHIONINE (MSEa)
5aa: SELENOMETHIONINE (MSEaa)
5ab: SELENOMETHIONINE (MSEab)
5ac: SELENOMETHIONINE (MSEac)
5ad: SELENOMETHIONINE (MSEad)
5ae: SELENOMETHIONINE (MSEae)
5af: SELENOMETHIONINE (MSEaf)
5ag: SELENOMETHIONINE (MSEag)
5ah: SELENOMETHIONINE (MSEah)
5ai: SELENOMETHIONINE (MSEai)
5aj: SELENOMETHIONINE (MSEaj)
5ak: SELENOMETHIONINE (MSEak)
5al: SELENOMETHIONINE (MSEal)
5am: SELENOMETHIONINE (MSEam)
5an: SELENOMETHIONINE (MSEan)
5ao: SELENOMETHIONINE (MSEao)
5ap: SELENOMETHIONINE (MSEap)
5aq: SELENOMETHIONINE (MSEaq)
5ar: SELENOMETHIONINE (MSEar)
5as: SELENOMETHIONINE (MSEas)
5at: SELENOMETHIONINE (MSEat)
5au: SELENOMETHIONINE (MSEau)
5av: SELENOMETHIONINE (MSEav)
5aw: SELENOMETHIONINE (MSEaw)
5ax: SELENOMETHIONINE (MSEax)
5ay: SELENOMETHIONINE (MSEay)
5az: SELENOMETHIONINE (MSEaz)
5b: SELENOMETHIONINE (MSEb)
5ba: SELENOMETHIONINE (MSEba)
5bb: SELENOMETHIONINE (MSEbb)
5bc: SELENOMETHIONINE (MSEbc)
5bd: SELENOMETHIONINE (MSEbd)
5be: SELENOMETHIONINE (MSEbe)
5bf: SELENOMETHIONINE (MSEbf)
5bg: SELENOMETHIONINE (MSEbg)
5bh: SELENOMETHIONINE (MSEbh)
5bi: SELENOMETHIONINE (MSEbi)
5bj: SELENOMETHIONINE (MSEbj)
5bk: SELENOMETHIONINE (MSEbk)
5bl: SELENOMETHIONINE (MSEbl)
5bm: SELENOMETHIONINE (MSEbm)
5bn: SELENOMETHIONINE (MSEbn)
5bo: SELENOMETHIONINE (MSEbo)
5bp: SELENOMETHIONINE (MSEbp)
5bq: SELENOMETHIONINE (MSEbq)
5br: SELENOMETHIONINE (MSEbr)
5bs: SELENOMETHIONINE (MSEbs)
5bt: SELENOMETHIONINE (MSEbt)
5c: SELENOMETHIONINE (MSEc)
5d: SELENOMETHIONINE (MSEd)
5e: SELENOMETHIONINE (MSEe)
5f: SELENOMETHIONINE (MSEf)
5g: SELENOMETHIONINE (MSEg)
5h: SELENOMETHIONINE (MSEh)
5i: SELENOMETHIONINE (MSEi)
5j: SELENOMETHIONINE (MSEj)
5k: SELENOMETHIONINE (MSEk)
5l: SELENOMETHIONINE (MSEl)
5m: SELENOMETHIONINE (MSEm)
5n: SELENOMETHIONINE (MSEn)
5o: SELENOMETHIONINE (MSEo)
5p: SELENOMETHIONINE (MSEp)
5q: SELENOMETHIONINE (MSEq)
5r: SELENOMETHIONINE (MSEr)
5s: SELENOMETHIONINE (MSEs)
5t: SELENOMETHIONINE (MSEt)
5u: SELENOMETHIONINE (MSEu)
5v: SELENOMETHIONINE (MSEv)
5w: SELENOMETHIONINE (MSEw)
5x: SELENOMETHIONINE (MSEx)
5y: SELENOMETHIONINE (MSEy)
5z: SELENOMETHIONINE (MSEz)
6a: SULFATE ION (SO4a)
6aa: SULFATE ION (SO4aa)
6ab: SULFATE ION (SO4ab)
6ac: SULFATE ION (SO4ac)
6ad: SULFATE ION (SO4ad)
6b: SULFATE ION (SO4b)
6c: SULFATE ION (SO4c)
6d: SULFATE ION (SO4d)
6e: SULFATE ION (SO4e)
6f: SULFATE ION (SO4f)
6g: SULFATE ION (SO4g)
6h: SULFATE ION (SO4h)
6i: SULFATE ION (SO4i)
6j: SULFATE ION (SO4j)
6k: SULFATE ION (SO4k)
6l: SULFATE ION (SO4l)
6m: SULFATE ION (SO4m)
6n: SULFATE ION (SO4n)
6o: SULFATE ION (SO4o)
6p: SULFATE ION (SO4p)
6q: SULFATE ION (SO4q)
6r: SULFATE ION (SO4r)
6s: SULFATE ION (SO4s)
6t: SULFATE ION (SO4t)
6u: SULFATE ION (SO4u)
6v: SULFATE ION (SO4v)
6w: SULFATE ION (SO4w)
6x: SULFATE ION (SO4x)
6y: SULFATE ION (SO4y)
6z: SULFATE ION (SO4z)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
16
Ligand/Ion
ACETATE ION
2
CL
1
Ligand/Ion
CHLORIDE ION
3
EPE
7
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4
GOL
3
Ligand/Ion
GLYCEROL
5
MSE
72
Mod. Amino Acid
SELENOMETHIONINE
6
SO4
30
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(57, 57)
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)
47: FC2 (SOFTWARE)
48: FC3 (SOFTWARE)
49: FC4 (SOFTWARE)
50: FC5 (SOFTWARE)
51: FC6 (SOFTWARE)
52: FC7 (SOFTWARE)
53: FC8 (SOFTWARE)
54: FC9 (SOFTWARE)
55: GC1 (SOFTWARE)
56: GC2 (SOFTWARE)
57: GC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PRO A:25 , ASP A:26 , LYS A:27 , THR B:239 , THR B:240 , LYS B:242
BINDING SITE FOR RESIDUE EPE A 400
02
AC2
SOFTWARE
THR A:239 , THR A:240 , PRO B:25 , ASP B:26 , LYS B:27
BINDING SITE FOR RESIDUE EPE B 400
03
AC3
SOFTWARE
PRO C:25 , ASP C:26 , LYS C:27 , THR D:239 , THR D:240 , LYS D:242
BINDING SITE FOR RESIDUE EPE D 400
04
AC4
SOFTWARE
PRO E:25 , ASP E:26 , LYS E:27 , THR F:239 , THR F:240 , LYS F:242 , HOH F:1273
BINDING SITE FOR RESIDUE EPE F 400
05
AC5
SOFTWARE
THR E:239 , THR E:240 , LYS E:242 , PRO F:25 , ASP F:26 , LYS F:27 , HOH F:1449
BINDING SITE FOR RESIDUE EPE F 349
06
AC6
SOFTWARE
PRO G:25 , ASP G:26 , LYS G:27 , HOH G:1097 , THR H:239 , THR H:240 , LYS H:242
BINDING SITE FOR RESIDUE EPE G 400
07
AC7
SOFTWARE
THR G:239 , THR G:240 , LYS G:242 , PRO H:25 , ASP H:26 , LYS H:27
BINDING SITE FOR RESIDUE EPE G 349
08
AC8
SOFTWARE
ARG F:42 , ARG F:45 , ACT F:351 , HOH F:1188
BINDING SITE FOR RESIDUE SO4 F 350
09
AC9
SOFTWARE
ARG B:42 , ARG B:45 , HOH B:1568
BINDING SITE FOR RESIDUE SO4 B 349
10
BC1
SOFTWARE
ARG D:42 , ARG D:45 , ACT D:353 , HOH D:900
BINDING SITE FOR RESIDUE SO4 D 349
11
BC2
SOFTWARE
ARG H:42 , ARG H:45 , HOH H:933
BINDING SITE FOR RESIDUE SO4 H 349
12
BC3
SOFTWARE
PHE A:23 , ARG A:166 , ASN A:167
BINDING SITE FOR RESIDUE SO4 A 349
13
BC4
SOFTWARE
ARG E:174 , HOH E:483 , HOH E:641 , HOH E:1456 , SER F:171
BINDING SITE FOR RESIDUE SO4 E 349
14
BC5
SOFTWARE
ARG C:174 , LEU D:169 , SER D:171 , HOH D:362
BINDING SITE FOR RESIDUE SO4 D 350
15
BC6
SOFTWARE
ARG E:42 , ARG E:45 , ACT E:353 , HOH E:1079
BINDING SITE FOR RESIDUE SO4 E 350
16
BC7
SOFTWARE
PHE G:23 , PRO G:62 , ARG G:166 , ASN G:167
BINDING SITE FOR RESIDUE SO4 G 350
17
BC8
SOFTWARE
ARG G:42 , ARG G:45 , ACT G:356 , HOH G:1317
BINDING SITE FOR RESIDUE SO4 G 351
18
BC9
SOFTWARE
ARG G:174 , LEU H:169 , SER H:171 , HOH H:546
BINDING SITE FOR RESIDUE SO4 H 350
19
CC1
SOFTWARE
ARG A:42 , ARG A:45 , LEU A:46 , HOH A:1594
BINDING SITE FOR RESIDUE SO4 A 350
20
CC2
SOFTWARE
ARG A:174 , LEU B:169 , SER B:171 , HOH B:646
BINDING SITE FOR RESIDUE SO4 B 350
21
CC3
SOFTWARE
GLN E:132 , LEU E:169 , HOH E:1087 , HOH E:1241 , HOH E:1523
BINDING SITE FOR RESIDUE SO4 E 351
22
CC4
SOFTWARE
PRO D:30 , ARG D:33
BINDING SITE FOR RESIDUE SO4 D 351
23
CC5
SOFTWARE
ARG D:42 , ARG D:45 , HOH D:1440
BINDING SITE FOR RESIDUE SO4 D 352
24
CC6
SOFTWARE
HIS C:232 , LYS C:248
BINDING SITE FOR RESIDUE SO4 C 349
25
CC7
SOFTWARE
ARG H:78 , ARG H:115
BINDING SITE FOR RESIDUE SO4 H 351
26
CC8
SOFTWARE
ARG G:247 , ASP G:251 , HOH G:1110
BINDING SITE FOR RESIDUE SO4 G 352
27
CC9
SOFTWARE
PRO B:30 , ARG B:33
BINDING SITE FOR RESIDUE SO4 B 351
28
DC1
SOFTWARE
PHE E:23 , PRO E:62 , ARG E:166 , ASN E:167 , HOH E:1333
BINDING SITE FOR RESIDUE SO4 E 352
29
DC2
SOFTWARE
ARG A:247
BINDING SITE FOR RESIDUE SO4 A 351
30
DC3
SOFTWARE
ARG B:78 , ARG B:115
BINDING SITE FOR RESIDUE SO4 B 352
31
DC4
SOFTWARE
ARG H:42 , ARG H:45
BINDING SITE FOR RESIDUE SO4 H 352
32
DC5
SOFTWARE
PHE C:23 , PRO C:62 , ARG C:166 , ASN C:167 , HOH C:376
BINDING SITE FOR RESIDUE SO4 C 350
33
DC6
SOFTWARE
PHE H:23 , PRO H:62 , ARG H:166 , ASN H:167 , PHE H:189 , HOH H:718
BINDING SITE FOR RESIDUE SO4 H 353
34
DC7
SOFTWARE
GLN G:132 , HOH G:451 , HOH G:1166
BINDING SITE FOR RESIDUE SO4 G 353
35
DC8
SOFTWARE
ARG G:78 , ARG G:115
BINDING SITE FOR RESIDUE SO4 G 354
36
DC9
SOFTWARE
HOH A:1065 , ARG C:42 , ARG C:45
BINDING SITE FOR RESIDUE SO4 A 352
37
EC1
SOFTWARE
ARG D:78 , LYS G:323 , ARG G:326
BINDING SITE FOR RESIDUE SO4 G 355
38
EC2
SOFTWARE
TRP D:288 , ASN D:292 , ILE D:293 , ASP D:294 , SO4 D:349 , HOH D:900
BINDING SITE FOR RESIDUE ACT D 353
39
EC3
SOFTWARE
LEU G:46 , TRP G:288 , ASN G:292 , ILE G:293 , ASP G:294 , SO4 G:351 , HOH G:1317
BINDING SITE FOR RESIDUE ACT G 356
40
EC4
SOFTWARE
TRP E:288 , ASN E:292 , ILE E:293 , ASP E:294 , SO4 E:350 , HOH E:1079
BINDING SITE FOR RESIDUE ACT E 353
41
EC5
SOFTWARE
TRP H:288 , ASN H:292 , ILE H:293 , ASP H:294 , HOH H:933
BINDING SITE FOR RESIDUE ACT H 354
42
EC6
SOFTWARE
LEU A:46 , TRP A:288 , ASN A:292 , ILE A:293 , ASP A:294 , HOH A:1594
BINDING SITE FOR RESIDUE ACT A 353
43
EC7
SOFTWARE
HOH A:1065 , LEU C:46 , TRP C:288 , ASN C:292 , ILE C:293 , ASP C:294
BINDING SITE FOR RESIDUE ACT C 351
44
EC8
SOFTWARE
TRP B:288 , ASN B:292 , ILE B:293 , ASP B:294 , HOH B:1568
BINDING SITE FOR RESIDUE ACT B 353
45
EC9
SOFTWARE
HIS C:295 , HOH C:868 , LYS D:238 , HOH D:1043
BINDING SITE FOR RESIDUE ACT C 352
46
FC1
SOFTWARE
TRP F:288 , ASN F:292 , ILE F:293 , ASP F:294 , SO4 F:350 , HOH F:1188
BINDING SITE FOR RESIDUE ACT F 351
47
FC2
SOFTWARE
ARG B:45
BINDING SITE FOR RESIDUE ACT B 354
48
FC3
SOFTWARE
ARG F:45
BINDING SITE FOR RESIDUE ACT F 352
49
FC4
SOFTWARE
HIS A:295 , HOH A:743 , LYS B:238 , HOH B:1042
BINDING SITE FOR RESIDUE ACT A 354
50
FC5
SOFTWARE
HIS G:295 , HOH G:1044 , LYS H:238
BINDING SITE FOR RESIDUE ACT G 357
51
FC6
SOFTWARE
HIS G:232
BINDING SITE FOR RESIDUE ACT G 358
52
FC7
SOFTWARE
LYS A:238 , HOH A:369 , HIS B:295
BINDING SITE FOR RESIDUE ACT A 355
53
FC8
SOFTWARE
HIS E:295 , HOH E:870 , HOH E:1139 , LYS F:238
BINDING SITE FOR RESIDUE ACT E 354
54
FC9
SOFTWARE
PHE F:23 , PRO F:62 , ARG F:166 , ASN F:167
BINDING SITE FOR RESIDUE GOL F 353
55
GC1
SOFTWARE
GLY C:178 , HIS C:179 , ALA C:180 , HOH C:401
BINDING SITE FOR RESIDUE GOL C 353
56
GC2
SOFTWARE
PHE D:23 , ARG D:166 , ASN D:167 , HOH D:619
BINDING SITE FOR RESIDUE GOL D 354
57
GC3
SOFTWARE
ASN B:167 , HOH B:1406
BINDING SITE FOR RESIDUE CL B 355
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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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
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 8)
Info
All SCOP Domains
1a: SCOP_d3s4ta_ (A:)
1b: SCOP_d3s4tb_ (B:)
1c: SCOP_d3s4tc_ (C:)
1d: SCOP_d3s4td_ (D:)
1e: SCOP_d3s4te_ (E:)
1f: SCOP_d3s4tf_ (F:)
1g: SCOP_d3s4tg_ (G:)
1h: SCOP_d3s4th_ (H:)
View:
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(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Metallo-dependent hydrolases
(273)
Family
:
PP1699/LP2961-like
(17)
Protein domain
:
automated matches
(1)
Polaromonas sp. [TaxId: 296591]
(1)
1a
d3s4ta_
A:
1b
d3s4tb_
B:
1c
d3s4tc_
C:
1d
d3s4td_
D:
1e
d3s4te_
E:
1f
d3s4tf_
F:
1g
d3s4tg_
G:
1h
d3s4th_
H:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
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Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Atom Selection
(currently selected atoms:
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Protein
Nucleic
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Sidechain
Hetero
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Chain D
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Asymmetric Unit 1
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select chains 'A' and 'C'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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Asym.Unit (921 KB)
Header - Asym.Unit
Biol.Unit 1 (456 KB)
Header - Biol.Unit 1
Biol.Unit 2 (234 KB)
Header - Biol.Unit 2
Biol.Unit 3 (232 KB)
Header - Biol.Unit 3
Biol.Unit 4 (458 KB)
Header - Biol.Unit 4
Biol.Unit 5 (232 KB)
Header - Biol.Unit 5
Biol.Unit 6 (234 KB)
Header - Biol.Unit 6
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