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1NGK
Asym. Unit
Info
Asym.Unit (316 KB)
Biol.Unit 1 (304 KB)
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(1)
Title
:
CRYSTALLOGRAPHIC STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS HEMOGLOBIN O
Authors
:
M. Milani, P. -Y. Savard, H. Oullet, P. Ascenzi, M. Guertin, M. Bolognesi
Date
:
17 Dec 02 (Deposition) - 20 May 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.11
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 (1x)
Keywords
:
Truncated Hemoglobin, Oxygen Storage/Transport Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Milani, P. -Y. Savard, H. Oullet, P. Ascenzi, M. Guertin, M. Bolognesi
A Tyrcd1/Trpg8 Hydrogen Bond Network And A Tyrb10-Tyrcd1 Covalent Link Shape The Heme Distal Site Of Mycobacterium Tuberculosis Hemoglobin O
Proc. Natl. Acad. Sci. Usa V. 100 5766 2003
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 42)
Info
All Hetero Components
1a: CYANIDE ION (CYNa)
1b: CYANIDE ION (CYNb)
1c: CYANIDE ION (CYNc)
1d: CYANIDE ION (CYNd)
1e: CYANIDE ION (CYNe)
1f: CYANIDE ION (CYNf)
1g: CYANIDE ION (CYNg)
1h: CYANIDE ION (CYNh)
1i: CYANIDE ION (CYNi)
1j: CYANIDE ION (CYNj)
1k: CYANIDE ION (CYNk)
1l: CYANIDE ION (CYNl)
2a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
2b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
2c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
2d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
2e: PROTOPORPHYRIN IX CONTAINING FE (HEMe)
2f: PROTOPORPHYRIN IX CONTAINING FE (HEMf)
2g: PROTOPORPHYRIN IX CONTAINING FE (HEMg)
2h: PROTOPORPHYRIN IX CONTAINING FE (HEMh)
2i: PROTOPORPHYRIN IX CONTAINING FE (HEMi)
2j: PROTOPORPHYRIN IX CONTAINING FE (HEMj)
2k: PROTOPORPHYRIN IX CONTAINING FE (HEMk)
2l: PROTOPORPHYRIN IX CONTAINING FE (HEMl)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
3h: SULFATE ION (SO4h)
3i: SULFATE ION (SO4i)
3j: SULFATE ION (SO4j)
3k: SULFATE ION (SO4k)
3l: SULFATE ION (SO4l)
3m: SULFATE ION (SO4m)
3n: SULFATE ION (SO4n)
3o: SULFATE ION (SO4o)
3p: SULFATE ION (SO4p)
3q: SULFATE ION (SO4q)
3r: SULFATE ION (SO4r)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CYN
12
Ligand/Ion
CYANIDE ION
2
HEM
12
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
3
SO4
18
Ligand/Ion
SULFATE 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 G:21
BINDING SITE FOR RESIDUE SO4 G 2001
02
AC2
SOFTWARE
ARG G:66 , HOH G:2068 , HOH G:2076 , HOH G:2106 , ARG K:66 , HOH K:842
BINDING SITE FOR RESIDUE SO4 G 2002
03
AC3
SOFTWARE
PRO E:59 , ARG E:60 , HOH E:1256 , ARG J:90
BINDING SITE FOR RESIDUE SO4 E 2003
04
AC4
SOFTWARE
PRO A:59 , ARG A:60 , GLU A:64
BINDING SITE FOR RESIDUE SO4 A 2004
05
AC5
SOFTWARE
ARG H:66 , HOH H:820 , ARG L:66 , ARG L:74 , HOH L:2020
BINDING SITE FOR RESIDUE SO4 L 2005
06
AC6
SOFTWARE
ASP E:40 , GLY E:43 , ARG E:47 , PRO L:59
BINDING SITE FOR RESIDUE SO4 E 2006
07
AC7
SOFTWARE
ASP B:40 , GLY B:43 , ARG B:47 , HOH B:2081 , HOH B:2132 , HOH B:2135 , PRO I:59 , ARG I:60
BINDING SITE FOR RESIDUE SO4 B 2007
08
AC8
SOFTWARE
ASP F:40 , ARG F:47 , PRO J:59 , ARG J:60
BINDING SITE FOR RESIDUE SO4 J 2008
09
AC9
SOFTWARE
ASP C:40 , ARG C:47 , HOH C:2067 , HOH C:2125 , PRO G:59 , ARG G:60
BINDING SITE FOR RESIDUE SO4 C 2009
10
BC1
SOFTWARE
ASP D:40 , ARG D:47 , HOH D:2138 , PRO K:59 , ARG K:60
BINDING SITE FOR RESIDUE SO4 D 2010
11
BC2
SOFTWARE
ASP A:40 , GLY A:43 , ARG A:47 , HOH A:2071 , HOH A:2148 , PRO H:59
BINDING SITE FOR RESIDUE SO4 A 2011
12
BC3
SOFTWARE
HIS A:93 , HOH A:2023 , HOH A:2029 , HOH A:2055 , ARG F:90
BINDING SITE FOR RESIDUE SO4 A 2012
13
BC4
SOFTWARE
ARG C:21 , HOH C:2177
BINDING SITE FOR RESIDUE SO4 C 2013
14
BC5
SOFTWARE
ARG A:21 , HOH A:2152
BINDING SITE FOR RESIDUE SO4 A 2014
15
BC6
SOFTWARE
ARG C:72 , ARG I:79 , HOH I:2135 , HOH I:2197 , ARG K:79
BINDING SITE FOR RESIDUE SO4 I 2015
16
BC7
SOFTWARE
HOH A:2087 , ARG G:79 , ARG L:79
BINDING SITE FOR RESIDUE SO4 A 2016
17
BC8
SOFTWARE
HOH B:2104 , HOH B:2118 , ARG H:79 , ARG J:79
BINDING SITE FOR RESIDUE SO4 B 2017
18
BC9
SOFTWARE
ARG I:74 , ARG J:66 , ARG J:74 , HOH J:2052 , HOH J:2113
BINDING SITE FOR RESIDUE SO4 J 2018
19
CC1
SOFTWARE
TYR A:23 , TYR A:36 , TRP A:88 , HEM A:700
BINDING SITE FOR RESIDUE CYN A 800
20
CC2
SOFTWARE
TYR B:23 , TYR B:36 , TRP B:88 , HEM B:700
BINDING SITE FOR RESIDUE CYN B 800
21
CC3
SOFTWARE
TYR C:23 , TYR C:36 , TRP C:88 , HEM C:700
BINDING SITE FOR RESIDUE CYN C 800
22
CC4
SOFTWARE
TYR D:23 , TYR D:36 , TRP D:88 , HEM D:700
BINDING SITE FOR RESIDUE CYN D 800
23
CC5
SOFTWARE
TYR E:23 , TYR E:36 , TRP E:88 , HEM E:700
BINDING SITE FOR RESIDUE CYN E 800
24
CC6
SOFTWARE
TYR F:23 , TYR F:36 , LEU F:48 , TRP F:88 , HEM F:700
BINDING SITE FOR RESIDUE CYN F 800
25
CC7
SOFTWARE
TYR G:36 , TRP G:88 , HEM G:700
BINDING SITE FOR RESIDUE CYN G 800
26
CC8
SOFTWARE
TYR H:36 , TRP H:88 , HEM H:700
BINDING SITE FOR RESIDUE CYN H 800
27
CC9
SOFTWARE
TYR I:36 , TRP I:88 , HEM I:700
BINDING SITE FOR RESIDUE CYN I 800
28
DC1
SOFTWARE
TYR J:23 , TYR J:36 , TRP J:88 , HEM J:700
BINDING SITE FOR RESIDUE CYN J 800
29
DC2
SOFTWARE
TYR K:36 , LEU K:48 , TRP K:88 , HEM K:700
BINDING SITE FOR RESIDUE CYN K 800
30
DC3
SOFTWARE
TYR L:36 , LEU L:48 , TRP L:88 , HEM L:700
BINDING SITE FOR RESIDUE CYN L 800
31
DC4
SOFTWARE
TYR A:36 , PRO A:37 , ALA A:44 , ARG A:47 , LEU A:48 , PHE A:51 , TYR A:62 , ARG A:66 , ARG A:74 , HIS A:75 , PHE A:78 , TRP A:88 , TYR A:115 , ALA A:119 , ALA A:120 , LEU A:123 , CYN A:800 , HOH A:2044 , HOH A:2048 , HOH A:2052 , HOH A:2058 , HOH H:821
BINDING SITE FOR RESIDUE HEM A 700
32
DC5
SOFTWARE
PRO B:37 , ARG B:47 , LEU B:48 , PHE B:51 , TYR B:62 , ARG B:66 , ARG B:74 , HIS B:75 , PHE B:78 , TRP B:88 , TYR B:115 , ALA B:119 , ALA B:120 , LEU B:123 , CYN B:800 , HOH B:2029 , HOH B:2038 , HOH B:2063 , HOH I:2107
BINDING SITE FOR RESIDUE HEM B 700
33
DC6
SOFTWARE
PRO C:37 , ALA C:44 , ARG C:47 , LEU C:48 , PHE C:51 , TYR C:62 , ARG C:66 , ARG C:74 , HIS C:75 , PHE C:78 , ILE C:80 , TRP C:88 , TYR C:115 , ALA C:119 , ALA C:120 , LEU C:123 , CYN C:800 , HOH C:2079 , HOH C:2105 , HOH C:2106 , HOH C:2125
BINDING SITE FOR RESIDUE HEM C 700
34
DC7
SOFTWARE
TYR D:36 , PRO D:37 , ALA D:44 , ARG D:47 , LEU D:48 , PHE D:51 , TYR D:62 , ARG D:66 , ARG D:74 , HIS D:75 , PHE D:78 , TRP D:88 , TYR D:115 , ALA D:119 , ALA D:120 , LEU D:123 , CYN D:800 , HOH D:2055 , HOH D:2063 , HOH D:2081 , HOH K:849
BINDING SITE FOR RESIDUE HEM D 700
35
DC8
SOFTWARE
PRO E:37 , ARG E:47 , LEU E:48 , PHE E:51 , TYR E:62 , ARG E:66 , ARG E:74 , HIS E:75 , PHE E:78 , ILE E:80 , TRP E:88 , TYR E:115 , ALA E:119 , ALA E:120 , LEU E:123 , HOH E:227 , HOH E:308 , CYN E:800 , HOH E:813 , HOH E:874 , HOH E:879
BINDING SITE FOR RESIDUE HEM E 700
36
DC9
SOFTWARE
TYR F:36 , PRO F:37 , ALA F:44 , ARG F:47 , LEU F:48 , PHE F:51 , TYR F:62 , ARG F:66 , ARG F:74 , HIS F:75 , PHE F:78 , TRP F:88 , TYR F:115 , ALA F:120 , LEU F:123 , CYN F:800 , HOH F:840 , HOH F:849 , HOH F:875 , HOH F:877 , HOH J:2044
BINDING SITE FOR RESIDUE HEM F 700
37
EC1
SOFTWARE
TYR G:36 , PRO G:37 , ARG G:47 , LEU G:48 , PHE G:51 , TYR G:62 , ARG G:66 , ARG G:74 , HIS G:75 , PHE G:78 , ILE G:80 , TRP G:88 , ALA G:119 , ALA G:120 , LEU G:123 , CYN G:800 , HOH G:2065 , HOH G:2080
BINDING SITE FOR RESIDUE HEM G 700
38
EC2
SOFTWARE
TYR H:36 , ALA H:44 , ARG H:47 , LEU H:48 , PHE H:51 , TYR H:62 , ARG H:66 , ARG H:74 , HIS H:75 , PHE H:78 , ILE H:80 , TRP H:88 , ALA H:119 , ALA H:120 , LEU H:123 , CYN H:800 , HOH H:823 , HOH H:850
BINDING SITE FOR RESIDUE HEM H 700
39
EC3
SOFTWARE
TYR I:36 , ALA I:44 , ARG I:47 , LEU I:48 , PHE I:51 , TYR I:62 , ARG I:66 , ARG I:74 , HIS I:75 , PHE I:78 , ILE I:80 , TRP I:88 , TYR I:115 , ALA I:119 , ALA I:120 , LEU I:123 , CYN I:800 , HOH I:2030 , HOH I:2033
BINDING SITE FOR RESIDUE HEM I 700
40
EC4
SOFTWARE
TYR J:36 , ALA J:44 , ARG J:47 , LEU J:48 , PHE J:51 , TYR J:62 , ARG J:66 , ARG J:74 , HIS J:75 , PHE J:78 , TRP J:88 , TYR J:115 , ALA J:119 , ALA J:120 , LEU J:123 , CYN J:800 , HOH J:2039 , HOH J:2047
BINDING SITE FOR RESIDUE HEM J 700
41
EC5
SOFTWARE
TYR K:36 , ASP K:40 , ALA K:44 , ARG K:47 , LEU K:48 , PHE K:51 , TYR K:62 , ARG K:66 , ARG K:74 , HIS K:75 , PHE K:78 , ILE K:80 , TRP K:88 , TYR K:115 , ALA K:119 , ALA K:120 , LEU K:123 , CYN K:800 , HOH K:832
BINDING SITE FOR RESIDUE HEM K 700
42
EC6
SOFTWARE
TYR L:36 , ALA L:44 , ARG L:47 , LEU L:48 , PHE L:51 , TYR L:62 , ARG L:66 , LEU L:71 , ARG L:74 , HIS L:75 , PHE L:78 , ILE L:80 , TRP L:88 , ALA L:119 , ALA L:120 , LEU L:123 , CYN L:800 , HOH L:2015
BINDING SITE FOR RESIDUE HEM L 700
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 12)
Info
All PROSITE Patterns/Profiles
1: GLOBIN_FAM_2 (A:51-75,B:51-75,C:51-75,D:51-75,E:...)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GLOBIN_FAM_2
PS01213
Protozoan/cyanobacterial globins signature.
TRHBO_MYCTO
51-75
12
A:51-75
B:51-75
C:51-75
D:51-75
E:51-75
F:51-75
G:51-75
H:51-75
I:51-75
J:51-75
K:51-75
L:51-75
TRHBO_MYCTU
51-75
12
A:51-75
B:51-75
C:51-75
D:51-75
E:51-75
F:51-75
G:51-75
H:51-75
I:51-75
J:51-75
K:51-75
L:51-75
[
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.
SCOP Domains
(1, 12)
Info
All SCOP Domains
1a: SCOP_d1ngka_ (A:)
1b: SCOP_d1ngkb_ (B:)
1c: SCOP_d1ngkc_ (C:)
1d: SCOP_d1ngkd_ (D:)
1e: SCOP_d1ngke_ (E:)
1f: SCOP_d1ngkf_ (F:)
1g: SCOP_d1ngkg_ (G:)
1h: SCOP_d1ngkh_ (H:)
1i: SCOP_d1ngki_ (I:)
1j: SCOP_d1ngkj_ (J:)
1k: SCOP_d1ngkk_ (K:)
1l: SCOP_d1ngkl_ (L:)
View:
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)
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Folds
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Superfamilies
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(
)
Families
(
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Globin-like
(1351)
Superfamily
:
Globin-like
(1308)
Family
:
Truncated hemoglobin
(27)
Protein domain
:
Protozoan/bacterial hemoglobin
(22)
Mycobacterium tuberculosis, HbO [TaxId: 1773]
(2)
1a
d1ngka_
A:
1b
d1ngkb_
B:
1c
d1ngkc_
C:
1d
d1ngkd_
D:
1e
d1ngke_
E:
1f
d1ngkf_
F:
1g
d1ngkg_
G:
1h
d1ngkh_
H:
1i
d1ngki_
I:
1j
d1ngkj_
J:
1k
d1ngkk_
K:
1l
d1ngkl_
L:
[
close SCOP info
]
CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_1ngkB00 (B:2-128)
1b: CATH_1ngkE00 (E:2-128)
1c: CATH_1ngkD00 (D:3-128)
1d: CATH_1ngkF00 (F:3-128)
1e: CATH_1ngkG00 (G:2-128)
1f: CATH_1ngkH00 (H:2-128)
1g: CATH_1ngkI00 (I:2-128)
1h: CATH_1ngkJ00 (J:2-128)
1i: CATH_1ngkK00 (K:2-128)
1j: CATH_1ngkL00 (L:2-128)
1k: CATH_1ngkA00 (A:3-128)
1l: CATH_1ngkC00 (C:3-128)
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Architectures
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(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Globin-like
(786)
Homologous Superfamily
:
Globins
(743)
Mycobacterium tuberculosis. Organism_taxid: 1773.
(2)
1a
1ngkB00
B:2-128
1b
1ngkE00
E:2-128
1c
1ngkD00
D:3-128
1d
1ngkF00
F:3-128
1e
1ngkG00
G:2-128
1f
1ngkH00
H:2-128
1g
1ngkI00
I:2-128
1h
1ngkJ00
J:2-128
1i
1ngkK00
K:2-128
1j
1ngkL00
L:2-128
1k
1ngkA00
A:3-128
1l
1ngkC00
C:3-128
[
close CATH info
]
Pfam Domains
(1, 12)
Info
all PFAM domains
1a: PFAM_Bac_globin_1ngkL01 (L:4-123)
1b: PFAM_Bac_globin_1ngkL02 (L:4-123)
1c: PFAM_Bac_globin_1ngkL03 (L:4-123)
1d: PFAM_Bac_globin_1ngkL04 (L:4-123)
1e: PFAM_Bac_globin_1ngkL05 (L:4-123)
1f: PFAM_Bac_globin_1ngkL06 (L:4-123)
1g: PFAM_Bac_globin_1ngkL07 (L:4-123)
1h: PFAM_Bac_globin_1ngkL08 (L:4-123)
1i: PFAM_Bac_globin_1ngkL09 (L:4-123)
1j: PFAM_Bac_globin_1ngkL10 (L:4-123)
1k: PFAM_Bac_globin_1ngkL11 (L:4-123)
1l: PFAM_Bac_globin_1ngkL12 (L:4-123)
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Clans
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Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Globin
(291)
Family
:
Bac_globin
(12)
Mycobacterium tuberculosis
(5)
1a
Bac_globin-1ngkL01
L:4-123
1b
Bac_globin-1ngkL02
L:4-123
1c
Bac_globin-1ngkL03
L:4-123
1d
Bac_globin-1ngkL04
L:4-123
1e
Bac_globin-1ngkL05
L:4-123
1f
Bac_globin-1ngkL06
L:4-123
1g
Bac_globin-1ngkL07
L:4-123
1h
Bac_globin-1ngkL08
L:4-123
1i
Bac_globin-1ngkL09
L:4-123
1j
Bac_globin-1ngkL10
L:4-123
1k
Bac_globin-1ngkL11
L:4-123
1l
Bac_globin-1ngkL12
L:4-123
[
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]
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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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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 (316 KB)
Header - Asym.Unit
Biol.Unit 1 (304 KB)
Header - Biol.Unit 1
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