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2ONM
Biol. Unit 2
Info
Asym.Unit (976 KB)
Biol.Unit 1 (333 KB)
Biol.Unit 2 (336 KB)
Biol.Unit 3 (322 KB)
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(1)
Title
:
HUMAN MITOCHONDRIAL ALDEHYDE DEHYDROGENASE ASIAN VARIANT, ALDH2*2, COMPLEXED WITH NAD+
Authors
:
H. N. Larson, T. D. Hurley
Date
:
24 Jan 07 (Deposition) - 06 Mar 07 (Release) - 12 Nov 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Biol. Unit 3: I,J,K,L (1x)
Keywords
:
Oxidoreductase, Aldh, Nad, Rossmann Fold
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. N. Larson, J. Zhou, Z. Chen, J. S. Stamler, H. Weiner, T. D. Hurley
Structural And Functional Consequences Of Coenzyme Binding To The Inactive Asian Variant Of Mitochondrial Aldehyde Dehydrogenase: Roles Of Residues 475 And 487.
J. Biol. Chem. V. 282 12940 2007
[
close entry info
]
Hetero Components
(4, 21)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
1b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
1c: ADENOSINE-5'-DIPHOSPHATE (ADPc)
1d: ADENOSINE-5'-DIPHOSPHATE (ADPd)
1e: ADENOSINE-5'-DIPHOSPHATE (ADPe)
1f: ADENOSINE-5'-DIPHOSPHATE (ADPf)
1g: ADENOSINE-5'-DIPHOSPHATE (ADPg)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
2l: 1,2-ETHANEDIOL (EDOl)
2m: 1,2-ETHANEDIOL (EDOm)
2n: 1,2-ETHANEDIOL (EDOn)
2o: 1,2-ETHANEDIOL (EDOo)
2p: 1,2-ETHANEDIOL (EDOp)
2q: 1,2-ETHANEDIOL (EDOq)
2r: 1,2-ETHANEDIOL (EDOr)
2s: 1,2-ETHANEDIOL (EDOs)
2t: 1,2-ETHANEDIOL (EDOt)
2u: 1,2-ETHANEDIOL (EDOu)
2v: 1,2-ETHANEDIOL (EDOv)
2w: 1,2-ETHANEDIOL (EDOw)
2x: 1,2-ETHANEDIOL (EDOx)
2y: 1,2-ETHANEDIOL (EDOy)
3a: GUANIDINE (GAIa)
3b: GUANIDINE (GAIb)
3c: GUANIDINE (GAIc)
3d: GUANIDINE (GAId)
3e: GUANIDINE (GAIe)
3f: GUANIDINE (GAIf)
3g: GUANIDINE (GAIg)
3h: GUANIDINE (GAIh)
3i: GUANIDINE (GAIi)
5a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
5b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
5c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
5d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
5e: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADe)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
4c: SODIUM ION (NAc)
4d: SODIUM ION (NAd)
5e: SODIUM ION (NAe)
5f: SODIUM ION (NAf)
5g: SODIUM ION (NAg)
5h: SODIUM ION (NAh)
5i: SODIUM ION (NAi)
5j: SODIUM ION (NAj)
5k: SODIUM ION (NAk)
5l: SODIUM ION (NAl)
5m: SODIUM ION (NAm)
5n: SODIUM ION (NAn)
5o: SODIUM ION (NAo)
5p: SODIUM ION (NAp)
5q: SODIUM ION (NAq)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
1
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
EDO
12
Ligand/Ion
1,2-ETHANEDIOL
3
GAI
5
Ligand/Ion
GUANIDINE
4
NA
-1
Ligand/Ion
SODIUM ION
5
NAD
3
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
[
close Hetero Component info
]
Sites
(28, 28)
Info
All Sites
01: AC3 (SOFTWARE)
02: AC4 (SOFTWARE)
03: BC1 (SOFTWARE)
04: BC2 (SOFTWARE)
05: BC3 (SOFTWARE)
06: BC4 (SOFTWARE)
07: CC4 (SOFTWARE)
08: CC5 (SOFTWARE)
09: CC6 (SOFTWARE)
10: CC7 (SOFTWARE)
11: DC7 (SOFTWARE)
12: EC2 (SOFTWARE)
13: EC3 (SOFTWARE)
14: EC4 (SOFTWARE)
15: EC5 (SOFTWARE)
16: EC6 (SOFTWARE)
17: EC7 (SOFTWARE)
18: EC8 (SOFTWARE)
19: EC9 (SOFTWARE)
20: FC1 (SOFTWARE)
21: FC2 (SOFTWARE)
22: FC3 (SOFTWARE)
23: FC4 (SOFTWARE)
24: GC2 (SOFTWARE)
25: GC3 (SOFTWARE)
26: GC4 (SOFTWARE)
27: GC8 (SOFTWARE)
28: GC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC3
SOFTWARE
GLY F:299 , PHE F:401 , GLY F:402
BINDING SITE FOR RESIDUE NA F 5007
02
AC4
SOFTWARE
ASN G:275 , ALA G:290 , ALA G:293 , GLY G:305 , THR G:308
BINDING SITE FOR RESIDUE NA G 5008
03
BC1
SOFTWARE
THR E:39 , VAL E:40 , ASP E:109 , GLN E:196
BINDING SITE FOR RESIDUE NA E 605
04
BC2
SOFTWARE
THR F:39 , VAL F:40 , ASP F:109 , GLN F:196 , HOH F:2029
BINDING SITE FOR RESIDUE NA F 606
05
BC3
SOFTWARE
THR G:39 , VAL G:40 , ASP G:109 , GLN G:196 , HOH G:2330
BINDING SITE FOR RESIDUE NA G 607
06
BC4
SOFTWARE
THR H:39 , VAL H:40 , ASP H:109 , GLN H:196 , HOH H:1859
BINDING SITE FOR RESIDUE NA H 608
07
CC4
SOFTWARE
ILE E:165 , ILE E:166 , TRP E:168 , LYS E:192 , GLU E:195 , GLN E:196 , GLY E:225 , GLY E:229 , ALA E:230 , PHE E:243 , GLY E:245 , SER E:246 , ILE E:249 , ILE E:253 , HOH E:1251 , HOH E:1286
BINDING SITE FOR RESIDUE ADP E 505
08
CC5
SOFTWARE
ILE F:165 , ILE F:166 , PRO F:167 , TRP F:168 , ASN F:169 , LYS F:192 , ALA F:194 , GLU F:195 , GLN F:196 , GLY F:225 , GLY F:229 , ALA F:230 , PHE F:243 , GLY F:245 , SER F:246 , ILE F:249 , ILE F:253 , GLU F:268 , LEU F:269 , GLY F:270 , CYS F:302 , GLN F:349 , LYS F:352 , GLU F:399 , PHE F:401 , HOH F:1015 , HOH F:1051 , HOH F:1652
BINDING SITE FOR RESIDUE NAD F 506
09
CC6
SOFTWARE
ILE G:165 , ILE G:166 , PRO G:167 , TRP G:168 , ASN G:169 , LYS G:192 , GLU G:195 , GLY G:225 , GLY G:229 , ALA G:230 , PHE G:243 , GLY G:245 , SER G:246 , ILE G:249 , ILE G:253 , LEU G:269 , GLY G:270 , CYS G:302 , GLN G:349 , LYS G:352 , GLU G:399 , PHE G:401
BINDING SITE FOR RESIDUE NAD G 507
10
CC7
SOFTWARE
ILE H:165 , ILE H:166 , PRO H:167 , TRP H:168 , ASN H:169 , LYS H:192 , GLU H:195 , GLY H:225 , GLY H:229 , ALA H:230 , PHE H:243 , GLY H:245 , SER H:246 , ILE H:249 , ILE H:253 , GLY H:270 , CYS H:302 , GLN H:349 , LYS H:352 , GLU H:399 , PHE H:401 , HOH H:1055
BINDING SITE FOR RESIDUE NAD H 508
11
DC7
SOFTWARE
ASP B:98 , TYR B:101 , TYR B:203 , HOH H:1184 , HOH H:2159
BINDING SITE FOR RESIDUE EDO B 902
12
EC2
SOFTWARE
TYR E:153 , ARG E:155 , ASN F:440 , SER F:443 , PHE H:151
BINDING SITE FOR RESIDUE EDO E 705
13
EC3
SOFTWARE
ASN E:41 , THR E:44 , GLU E:46 , ILE E:48
BINDING SITE FOR RESIDUE EDO E 805
14
EC4
SOFTWARE
PHE E:18 , TYR E:101 , TYR E:203 , HOH E:2787 , GLN I:14
BINDING SITE FOR RESIDUE EDO E 905
15
EC5
SOFTWARE
SER E:443 , TYR F:153 , ARG F:155 , PHE G:151
BINDING SITE FOR RESIDUE EDO F 706
16
EC6
SOFTWARE
GLN F:14 , ASN F:41 , THR F:44 , GLU F:46 , LEU F:108 , HOH F:2389
BINDING SITE FOR RESIDUE EDO F 806
17
EC7
SOFTWARE
PHE F:18 , TYR F:101 , TYR F:203 , HOH F:2346
BINDING SITE FOR RESIDUE EDO F 906
18
EC8
SOFTWARE
PHE F:151 , TYR G:153 , ARG G:155 , ASN H:440 , SER H:443
BINDING SITE FOR RESIDUE EDO F 707
19
EC9
SOFTWARE
ASN G:41 , THR G:44 , ILE G:48 , LEU G:108 , HOH G:2633
BINDING SITE FOR RESIDUE EDO G 807
20
FC1
SOFTWARE
TYR G:101 , HOH G:2909
BINDING SITE FOR RESIDUE EDO G 907
21
FC2
SOFTWARE
PHE E:151 , ASN G:440 , SER G:443 , TYR H:153 , ARG H:155
BINDING SITE FOR RESIDUE EDO H 708
22
FC3
SOFTWARE
ASN H:41 , THR H:44 , GLU H:46 , HOH H:2123
BINDING SITE FOR RESIDUE EDO H 808
23
FC4
SOFTWARE
LEU D:367 , PHE H:18 , ASP H:98 , TYR H:101 , TYR H:203 , HOH H:1772 , HOH H:2005
BINDING SITE FOR RESIDUE EDO H 908
24
GC2
SOFTWARE
ASP E:147 , PHE E:150 , PHE F:459 , HOH F:2713
BINDING SITE FOR RESIDUE GAI E 906
25
GC3
SOFTWARE
ILE G:146 , ASP G:147 , PHE G:150 , HOH G:2440 , HOH G:2819 , PHE H:459
BINDING SITE FOR RESIDUE GAI G 5009
26
GC4
SOFTWARE
PHE G:459 , ILE H:146 , ASP H:147 , PHE H:150 , HOH H:2313
BINDING SITE FOR RESIDUE GAI H 909
27
GC8
SOFTWARE
ASN E:440 , HOH E:2847 , ASN H:440
BINDING SITE FOR RESIDUE GAI E 907
28
GC9
SOFTWARE
ASN F:440 , HOH F:1342 , ASN G:440 , HOH G:1845
BINDING SITE FOR RESIDUE GAI G 5010
[
close Site info
]
SAPs(SNPs)/Variants
(3, 12)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_011869 (E320V, chain E/F/G/H, )
2: VAR_011302 (E479K, chain E/F/G/H, )
3: VAR_002248 (K487K, chain E/F/G/H, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_011869
E
337
V
ALDH2_HUMAN
Polymorphism
1062136
E/F/G/H
E
320
V
2
UniProt
VAR_011302
E
496
K
ALDH2_HUMAN
Polymorphism
---
E/F/G/H
E
479
K
3
UniProt
VAR_002248
E
504
K
ALDH2_HUMAN
Polymorphism
671
E/F/G/H
K
487
K
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: ALDEHYDE_DEHYDR_GLU (E:267-274,F:267-274,G:267-274,H:26...)
2: ALDEHYDE_DEHYDR_CYS (E:295-306,F:295-306,G:295-306,H:29...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ALDEHYDE_DEHYDR_GLU
PS00687
Aldehyde dehydrogenases glutamic acid active site.
ALDH2_HUMAN
284-291
4
-
-
-
-
E:267-274
F:267-274
G:267-274
H:267-274
-
-
-
-
2
ALDEHYDE_DEHYDR_CYS
PS00070
Aldehyde dehydrogenases cysteine active site.
ALDH2_HUMAN
312-323
4
-
-
-
-
E:295-306
F:295-306
G:295-306
H:295-306
-
-
-
-
[
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_d2onma_ (A:)
1b: SCOP_d2onmb_ (B:)
1c: SCOP_d2onmc_ (C:)
1d: SCOP_d2onmd_ (D:)
1e: SCOP_d2onme_ (E:)
1f: SCOP_d2onmf_ (F:)
1g: SCOP_d2onmg_ (G:)
1h: SCOP_d2onmh_ (H:)
1i: SCOP_d2onmi_ (I:)
1j: SCOP_d2onmj_ (J:)
1k: SCOP_d2onmk_ (K:)
1l: SCOP_d2onml_ (L:)
View:
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Superfamilies
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Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
ALDH-like
(168)
Superfamily
:
ALDH-like
(168)
Family
:
ALDH-like
(76)
Protein domain
:
Aldehyde reductase (dehydrogenase), ALDH
(39)
Human (Homo sapiens), mitochondrial [TaxId: 9606]
(25)
1a
d2onma_
A:
1b
d2onmb_
B:
1c
d2onmc_
C:
1d
d2onmd_
D:
1e
d2onme_
E:
1f
d2onmf_
F:
1g
d2onmg_
G:
1h
d2onmh_
H:
1i
d2onmi_
I:
1j
d2onmj_
J:
1k
d2onmk_
K:
1l
d2onml_
L:
[
close SCOP info
]
CATH Domains
(2, 24)
Info
all CATH domains
1a: CATH_2onmA01 (A:8-270,A:461-500)
1b: CATH_2onmE01 (E:8-270,E:461-500)
1c: CATH_2onmF01 (F:8-270,F:461-500)
1d: CATH_2onmG01 (G:8-270,G:461-500)
1e: CATH_2onmH01 (H:8-270,H:461-500)
1f: CATH_2onmI01 (I:8-270,I:461-500)
1g: CATH_2onmJ01 (J:8-270,J:461-500)
1h: CATH_2onmK01 (K:8-270,K:461-500)
1i: CATH_2onmL01 (L:8-270,L:461-500)
1j: CATH_2onmB01 (B:8-270,B:461-500)
1k: CATH_2onmC01 (C:8-270,C:461-500)
1l: CATH_2onmD01 (D:8-270,D:461-500)
2a: CATH_2onmA02 (A:271-460)
2b: CATH_2onmB02 (B:271-460)
2c: CATH_2onmC02 (C:271-460)
2d: CATH_2onmD02 (D:271-460)
2e: CATH_2onmE02 (E:271-460)
2f: CATH_2onmF02 (F:271-460)
2g: CATH_2onmG02 (G:271-460)
2h: CATH_2onmH02 (H:271-460)
2i: CATH_2onmI02 (I:271-460)
2j: CATH_2onmJ02 (J:271-460)
2k: CATH_2onmK02 (K:271-460)
2l: CATH_2onmL02 (L:271-460)
View:
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Architectures
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Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Aldehyde Dehydrogenase; Chain A, domain 1
(86)
Homologous Superfamily
:
Aldehyde Dehydrogenase; Chain A, domain 1
(86)
Human (Homo sapiens)
(22)
1a
2onmA01
A:8-270,A:461-500
1b
2onmE01
E:8-270,E:461-500
1c
2onmF01
F:8-270,F:461-500
1d
2onmG01
G:8-270,G:461-500
1e
2onmH01
H:8-270,H:461-500
1f
2onmI01
I:8-270,I:461-500
1g
2onmJ01
J:8-270,J:461-500
1h
2onmK01
K:8-270,K:461-500
1i
2onmL01
L:8-270,L:461-500
1j
2onmB01
B:8-270,B:461-500
1k
2onmC01
C:8-270,C:461-500
1l
2onmD01
D:8-270,D:461-500
Topology
:
Aldehyde Dehydrogenase; Chain A, domain 2
(89)
Homologous Superfamily
:
Aldehyde Dehydrogenase; Chain A, domain 2
(89)
Human (Homo sapiens)
(22)
2a
2onmA02
A:271-460
2b
2onmB02
B:271-460
2c
2onmC02
C:271-460
2d
2onmD02
D:271-460
2e
2onmE02
E:271-460
2f
2onmF02
F:271-460
2g
2onmG02
G:271-460
2h
2onmH02
H:271-460
2i
2onmI02
I:271-460
2j
2onmJ02
J:271-460
2k
2onmK02
K:271-460
2l
2onmL02
L:271-460
[
close CATH info
]
Pfam Domains
(1, 12)
Info
all PFAM domains
1a: PFAM_Aldedh_2onmL01 (L:28-491)
1b: PFAM_Aldedh_2onmL02 (L:28-491)
1c: PFAM_Aldedh_2onmL03 (L:28-491)
1d: PFAM_Aldedh_2onmL04 (L:28-491)
1e: PFAM_Aldedh_2onmL05 (L:28-491)
1f: PFAM_Aldedh_2onmL06 (L:28-491)
1g: PFAM_Aldedh_2onmL07 (L:28-491)
1h: PFAM_Aldedh_2onmL08 (L:28-491)
1i: PFAM_Aldedh_2onmL09 (L:28-491)
1j: PFAM_Aldedh_2onmL10 (L:28-491)
1k: PFAM_Aldedh_2onmL11 (L:28-491)
1l: PFAM_Aldedh_2onmL12 (L:28-491)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
ALDH-like
(49)
Family
:
Aldedh
(45)
Homo sapiens (Human)
(21)
1a
Aldedh-2onmL01
L:28-491
1b
Aldedh-2onmL02
L:28-491
1c
Aldedh-2onmL03
L:28-491
1d
Aldedh-2onmL04
L:28-491
1e
Aldedh-2onmL05
L:28-491
1f
Aldedh-2onmL06
L:28-491
1g
Aldedh-2onmL07
L:28-491
1h
Aldedh-2onmL08
L:28-491
1i
Aldedh-2onmL09
L:28-491
1j
Aldedh-2onmL10
L:28-491
1k
Aldedh-2onmL11
L:28-491
1l
Aldedh-2onmL12
L:28-491
[
close Pfam info
]
Atom Selection
(currently selected atoms:
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Sidechain
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All Atoms
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Protein & NOT Site
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Chain G
Chain H
Asymmetric Unit 1
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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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