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3E1O
Biol. Unit 1
Info
Asym.Unit (336 KB)
Biol.Unit 1 (637 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF E. COLI BACTERIOFERRITIN (BFR) WITH TWO ZN(II) ION SITES AT THE FERROXIDASE CENTRE (ZN-BFR).
Authors
:
A. Crow, T. Lawson, A. Lewin, G. R. Moore, N. Le Brun
Date
:
04 Aug 08 (Deposition) - 05 May 09 (Release) - 26 May 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.95
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L (2x)
Keywords
:
Bacterioferritin. Rhombic Dodecahedral Superstructure. , Heme, Iron, Iron Storage, Metal-Binding, Metal Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Crow, T. L. Lawson, A. Lewin, G. R. Moore, N. E. Le Brun
Structural Basis For Iron Mineralization By Bacterioferritin
J. Am. Chem. Soc. V. 131 6808 2009
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 44)
Info
All Hetero Components
1a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
1b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
1c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
1d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
1e: PROTOPORPHYRIN IX CONTAINING FE (HEMe)
1f: PROTOPORPHYRIN IX CONTAINING FE (HEMf)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
2g: SULFATE ION (SO4g)
2h: SULFATE ION (SO4h)
2i: SULFATE ION (SO4i)
2j: SULFATE ION (SO4j)
2k: SULFATE ION (SO4k)
2l: SULFATE ION (SO4l)
2m: SULFATE ION (SO4m)
2n: SULFATE ION (SO4n)
2o: SULFATE ION (SO4o)
2p: SULFATE ION (SO4p)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
3e: ZINC ION (ZNe)
3f: ZINC ION (ZNf)
3g: ZINC ION (ZNg)
3h: ZINC ION (ZNh)
3i: ZINC ION (ZNi)
3j: ZINC ION (ZNj)
3k: ZINC ION (ZNk)
3l: ZINC ION (ZNl)
3m: ZINC ION (ZNm)
3n: ZINC ION (ZNn)
3o: ZINC ION (ZNo)
3p: ZINC ION (ZNp)
3q: ZINC ION (ZNq)
3r: ZINC ION (ZNr)
3s: ZINC ION (ZNs)
3t: ZINC ION (ZNt)
3u: ZINC ION (ZNu)
3v: ZINC ION (ZNv)
3w: ZINC ION (ZNw)
3x: ZINC ION (ZNx)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
HEM
12
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
2
SO4
32
Ligand/Ion
SULFATE ION
3
ZN
-1
Ligand/Ion
ZINC 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
GLY A:145 , LEU A:146 , GLN A:147
BINDING SITE FOR RESIDUE SO4 A 250
02
AC2
SOFTWARE
GLU A:18 , GLU A:51 , HIS A:54 , GLU A:127
BINDING SITE FOR RESIDUE ZN A 300
03
AC3
SOFTWARE
GLU A:51 , GLU A:94 , GLU A:127 , HIS A:130
BINDING SITE FOR RESIDUE ZN A 301
04
AC4
SOFTWARE
ARG A:117 , ARG D:117 , ARG J:117 , HOH J:319
BINDING SITE FOR RESIDUE SO4 A 302
05
AC5
SOFTWARE
ILE A:22 , ASN A:23 , PHE A:26 , TYR A:45 , ILE A:49 , MET A:52 , ALA A:55 , ASP A:56 , HOH A:311 , LEU B:19 , ASN B:23 , PHE B:26 , TYR B:45 , MET B:52 , HOH B:319
BINDING SITE FOR RESIDUE HEM A 200
06
AC6
SOFTWARE
GLY B:145 , LEU B:146 , GLN B:147
BINDING SITE FOR RESIDUE SO4 B 250
07
AC7
SOFTWARE
GLU B:18 , GLU B:51 , HIS B:54 , GLU B:127
BINDING SITE FOR RESIDUE ZN B 300
08
AC8
SOFTWARE
GLU B:51 , GLU B:94 , GLU B:127 , HIS B:130
BINDING SITE FOR RESIDUE ZN B 301
09
AC9
SOFTWARE
GLY C:145 , LEU C:146 , GLN C:147
BINDING SITE FOR RESIDUE SO4 C 250
10
BC1
SOFTWARE
GLU C:18 , GLU C:51 , HIS C:54 , GLU C:127
BINDING SITE FOR RESIDUE ZN C 300
11
BC2
SOFTWARE
GLU C:51 , GLU C:94 , GLU C:127 , HIS C:130
BINDING SITE FOR RESIDUE ZN C 301
12
BC3
SOFTWARE
ARG B:117 , ARG C:117 , HOH C:316 , ARG H:117
BINDING SITE FOR RESIDUE SO4 C 302
13
BC4
SOFTWARE
GLY D:145 , LEU D:146 , GLN D:147
BINDING SITE FOR RESIDUE SO4 D 250
14
BC5
SOFTWARE
GLU D:18 , GLU D:51 , HIS D:54 , GLU D:127
BINDING SITE FOR RESIDUE ZN D 300
15
BC6
SOFTWARE
GLU D:51 , GLU D:94 , GLU D:127 , HIS D:130
BINDING SITE FOR RESIDUE ZN D 301
16
BC7
SOFTWARE
ILE C:22 , ASN C:23 , PHE C:26 , TYR C:45 , ILE C:49 , MET C:52 , ALA C:55 , HOH C:308 , LEU D:19 , ASN D:23 , PHE D:26 , TYR D:45 , MET D:52 , HOH D:309
BINDING SITE FOR RESIDUE HEM D 200
17
BC8
SOFTWARE
GLY E:145 , LEU E:146 , GLN E:147
BINDING SITE FOR RESIDUE SO4 E 250
18
BC9
SOFTWARE
GLU E:18 , GLU E:51 , HIS E:54 , GLU E:127
BINDING SITE FOR RESIDUE ZN E 300
19
CC1
SOFTWARE
GLU E:51 , GLU E:94 , GLU E:127 , HIS E:130
BINDING SITE FOR RESIDUE ZN E 301
20
CC2
SOFTWARE
ASN E:23 , PHE E:26 , TYR E:45 , ILE E:49 , MET E:52 , ALA E:55 , ASP E:56 , HOH E:314 , LEU F:19 , ILE F:22 , ASN F:23 , PHE F:26 , TYR F:45 , MET F:52 , HOH F:311
BINDING SITE FOR RESIDUE HEM E 200
21
CC3
SOFTWARE
GLY F:145 , LEU F:146 , GLN F:147
BINDING SITE FOR RESIDUE SO4 F 250
22
CC4
SOFTWARE
GLU F:18 , GLU F:51 , HIS F:54 , GLU F:127
BINDING SITE FOR RESIDUE ZN F 300
23
CC5
SOFTWARE
GLU F:51 , GLU F:94 , GLU F:127 , HIS F:130
BINDING SITE FOR RESIDUE ZN F 301
24
CC6
SOFTWARE
ARG F:117 , HOH F:323 , ARG I:117 , ARG K:117
BINDING SITE FOR RESIDUE SO4 F 302
25
CC7
SOFTWARE
GLY G:145 , LEU G:146 , GLN G:147
BINDING SITE FOR RESIDUE SO4 G 250
26
CC8
SOFTWARE
GLU G:18 , GLU G:51 , HIS G:54 , GLU G:127
BINDING SITE FOR RESIDUE ZN G 300
27
CC9
SOFTWARE
GLU G:51 , GLU G:94 , GLU G:127 , HIS G:130
BINDING SITE FOR RESIDUE ZN G 301
28
DC1
SOFTWARE
ARG E:117 , ARG G:117 , ARG L:117
BINDING SITE FOR RESIDUE SO4 G 302
29
DC2
SOFTWARE
GLY H:145 , LEU H:146 , GLN H:147
BINDING SITE FOR RESIDUE SO4 H 250
30
DC3
SOFTWARE
GLU H:18 , GLU H:51 , HIS H:54 , GLU H:127
BINDING SITE FOR RESIDUE ZN H 300
31
DC4
SOFTWARE
GLU H:51 , GLU H:94 , GLU H:127 , HIS H:130
BINDING SITE FOR RESIDUE ZN H 301
32
DC5
SOFTWARE
ILE G:22 , ASN G:23 , PHE G:26 , TYR G:45 , MET G:52 , ALA G:55 , HOH G:311 , LEU H:19 , ASN H:23 , PHE H:26 , TYR H:45 , MET H:52 , HOH H:306
BINDING SITE FOR RESIDUE HEM H 200
33
DC6
SOFTWARE
GLY I:145 , LEU I:146 , GLN I:147
BINDING SITE FOR RESIDUE SO4 I 250
34
DC7
SOFTWARE
GLU I:18 , GLU I:51 , HIS I:54 , GLU I:127
BINDING SITE FOR RESIDUE ZN I 300
35
DC8
SOFTWARE
GLU I:51 , GLU I:94 , GLU I:127 , HIS I:130
BINDING SITE FOR RESIDUE ZN I 301
36
DC9
SOFTWARE
ILE I:22 , ASN I:23 , PHE I:26 , TYR I:45 , ILE I:49 , MET I:52 , ALA I:55 , LEU J:19 , ASN J:23 , PHE J:26 , TYR J:45 , ILE J:49 , MET J:52 , HOH J:309 , HOH J:310
BINDING SITE FOR RESIDUE HEM I 200
37
EC1
SOFTWARE
GLY J:145 , LEU J:146 , GLN J:147
BINDING SITE FOR RESIDUE SO4 J 250
38
EC2
SOFTWARE
GLU J:18 , GLU J:51 , HIS J:54 , GLU J:127
BINDING SITE FOR RESIDUE ZN J 300
39
EC3
SOFTWARE
GLU J:51 , GLU J:94 , GLU J:127 , HIS J:130
BINDING SITE FOR RESIDUE ZN J 301
40
EC4
SOFTWARE
GLY K:145 , LEU K:146 , GLN K:147
BINDING SITE FOR RESIDUE SO4 K 250
41
EC5
SOFTWARE
GLU K:18 , GLU K:51 , HIS K:54 , GLU K:127
BINDING SITE FOR RESIDUE ZN K 300
42
EC6
SOFTWARE
GLU K:51 , GLU K:94 , GLU K:127 , HIS K:130
BINDING SITE FOR RESIDUE ZN K 301
43
EC7
SOFTWARE
ILE K:22 , ASN K:23 , PHE K:26 , TYR K:45 , ILE K:49 , MET K:52 , ALA K:55 , ASP K:56 , HOH K:317 , LEU L:19 , ILE L:22 , ASN L:23 , PHE L:26 , TYR L:45 , MET L:52 , HOH L:306
BINDING SITE FOR RESIDUE HEM K 200
44
EC8
SOFTWARE
GLY L:145 , LEU L:146 , GLN L:147
BINDING SITE FOR RESIDUE SO4 L 250
45
EC9
SOFTWARE
GLU L:18 , GLU L:51 , HIS L:54 , GLU L:127
BINDING SITE FOR RESIDUE ZN L 300
46
FC1
SOFTWARE
GLU L:51 , GLU L:94 , GLU L:127 , HIS L:130
BINDING SITE FOR RESIDUE ZN L 301
[
close Site info
]
SAPs(SNPs)/Variants
(10, 240)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_BFR_ECOLI_001 (K38M, chain A/B/C/D/E/F/G/H/I/J/K/L, )
02: VAR_BFR_ECOLI_002 (R57K, chain A/B/C/D/E/F/G/H/I/J/K/L, )
03: VAR_BFR_ECOLI_003 (L68I, chain A/B/C/D/E/F/G/H/I/J/K/L, )
04: VAR_BFR_ECOLI_004 (N78G, chain A/B/C/D/E/F/G/H/I/J/K/L, )
05: VAR_BFR_ECOLI_005 (R88Q, chain A/B/C/D/E/F/G/H/I/J/K/L, )
06: VAR_BFR_ECOLI_006 (A92R, chain A/B/C/D/E/F/G/H/I/J/K/L, )
07: VAR_BFR_ECOLI_007 (D96E, chain A/B/C/D/E/F/G/H/I/J/K/L, )
08: VAR_BFR_ECOLI_008 (N100D, chain A/B/C/D/E/F/G/H/I/J/K/L, )
09: VAR_BFR_ECOLI_009 (G106A, chain A/B/C/D/E/F/G/H/I/J/K/L, )
10: VAR_BFR_ECOLI_010 (R125A, chain A/B/C/D/E/F/G/H/I/J/K/L, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_BFR_ECOLI_001
*
K
38
M
BFR_ECOLI
---
---
A/B/C/D/E/F/G/H/I/J/K/L
K
38
M
02
UniProt
VAR_BFR_ECOLI_002
*
R
57
K
BFR_ECOLI
---
---
A/B/C/D/E/F/G/H/I/J/K/L
R
57
K
03
UniProt
VAR_BFR_ECOLI_003
*
L
68
I
BFR_ECOLI
---
---
A/B/C/D/E/F/G/H/I/J/K/L
L
68
I
04
UniProt
VAR_BFR_ECOLI_004
*
N
78
G
BFR_ECOLI
---
---
A/B/C/D/E/F/G/H/I/J/K/L
N
78
G
05
UniProt
VAR_BFR_ECOLI_005
*
R
88
Q
BFR_ECOLI
---
---
A/B/C/D/E/F/G/H/I/J/K/L
R
88
Q
06
UniProt
VAR_BFR_ECOLI_006
*
A
92
R
BFR_ECOLI
---
---
A/B/C/D/E/F/G/H/I/J/K/L
A
92
R
07
UniProt
VAR_BFR_ECOLI_007
*
D
96
E
BFR_ECOLI
---
---
A/B/C/D/E/F/G/H/I/J/K/L
D
96
E
08
UniProt
VAR_BFR_ECOLI_008
*
N
100
D
BFR_ECOLI
---
---
A/B/C/D/E/F/G/H/I/J/K/L
N
100
D
09
UniProt
VAR_BFR_ECOLI_009
*
G
106
A
BFR_ECOLI
---
---
A/B/C/D/E/F/G/H/I/J/K/L
G
106
A
10
UniProt
VAR_BFR_ECOLI_010
*
R
125
A
BFR_ECOLI
---
---
A/B/C/D/E/F/G/H/I/J/K/L
R
125
A
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 48)
Info
All PROSITE Patterns/Profiles
1: BACTERIOFERRITIN (A:1-19,B:1-19,C:1-19,D:1-19,E:1-19...)
2: FERRITIN_LIKE (A:1-145,B:1-145,C:1-145,D:1-145,E:...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
BACTERIOFERRITIN
PS00549
Bacterioferritin signature.
BFR_ECOLI
1-19
24
A:1-19
B:1-19
C:1-19
D:1-19
E:1-19
F:1-19
G:1-19
H:1-19
I:1-19
J:1-19
K:1-19
L:1-19
2
FERRITIN_LIKE
PS50905
Ferritin-like diiron domain profile.
BFR_ECOLI
1-145
24
A:1-145
B:1-145
C:1-145
D:1-145
E:1-145
F:1-145
G:1-145
H:1-145
I:1-145
J:1-145
K:1-145
L:1-145
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 12)
Info
All SCOP Domains
1a: SCOP_d3e1oa_ (A:)
1b: SCOP_d3e1ob_ (B:)
1c: SCOP_d3e1oc_ (C:)
1d: SCOP_d3e1od_ (D:)
1e: SCOP_d3e1oe_ (E:)
1f: SCOP_d3e1of_ (F:)
1g: SCOP_d3e1og_ (G:)
1h: SCOP_d3e1oh_ (H:)
1i: SCOP_d3e1oi_ (I:)
1j: SCOP_d3e1oj_ (J:)
1k: SCOP_d3e1ok_ (K:)
1l: SCOP_d3e1ol_ (L:)
View:
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)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Ferritin-like
(533)
Superfamily
:
Ferritin-like
(489)
Family
:
Ferritin
(232)
Protein domain
:
Bacterioferritin (cytochrome b1)
(19)
Escherichia coli [TaxId: 562]
(11)
1a
d3e1oa_
A:
1b
d3e1ob_
B:
1c
d3e1oc_
C:
1d
d3e1od_
D:
1e
d3e1oe_
E:
1f
d3e1of_
F:
1g
d3e1og_
G:
1h
d3e1oh_
H:
1i
d3e1oi_
I:
1j
d3e1oj_
J:
1k
d3e1ok_
K:
1l
d3e1ol_
L:
[
close SCOP info
]
CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_3e1oA00 (A:1-156)
1b: CATH_3e1oB00 (B:1-156)
1c: CATH_3e1oC00 (C:1-156)
1d: CATH_3e1oD00 (D:1-156)
1e: CATH_3e1oE00 (E:1-156)
1f: CATH_3e1oF00 (F:1-156)
1g: CATH_3e1oG00 (G:1-156)
1h: CATH_3e1oH00 (H:1-156)
1i: CATH_3e1oI00 (I:1-156)
1j: CATH_3e1oJ00 (J:1-156)
1k: CATH_3e1oK00 (K:1-156)
1l: CATH_3e1oL00 (L:1-156)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Ferritin;
(180)
Homologous Superfamily
:
[code=1.20.1260.10, no name defined]
(180)
Escherichia coli. Organism_taxid: 83333. Strain: k-12.
(7)
1a
3e1oA00
A:1-156
1b
3e1oB00
B:1-156
1c
3e1oC00
C:1-156
1d
3e1oD00
D:1-156
1e
3e1oE00
E:1-156
1f
3e1oF00
F:1-156
1g
3e1oG00
G:1-156
1h
3e1oH00
H:1-156
1i
3e1oI00
I:1-156
1j
3e1oJ00
J:1-156
1k
3e1oK00
K:1-156
1l
3e1oL00
L:1-156
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
Chain I
Chain J
Chain K
Chain L
Asymmetric Unit 1
Asymmetric Unit 2
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(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
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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Log
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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Asym.Unit (336 KB)
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Biol.Unit 1 (637 KB)
Header - Biol.Unit 1
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