PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
Getting 'PROSITE' information from database.
3INL
Biol. Unit 1
Info
Asym.Unit (690 KB)
Biol.Unit 1 (344 KB)
Biol.Unit 2 (347 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
HUMAN MITOCHONDRIAL ALDEHYDE DEHYDROGENASE ASIAN VARIANT, ALDH2*2, COMPLEXED WITH AGONIST ALDA-1
Authors
:
S. Perez-Miller, T. D. Hurley
Date
:
12 Aug 09 (Deposition) - 12 Jan 10 (Release) - 11 Aug 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.86
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Keywords
:
Oxidoreductase, Aldh, E487K, Rossmann Fold, Alda-1, Activator, Mitochondrion, Nad, Transit Peptide
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Perez-Miller, H. Younus, R. Vanam, C. H. Chen, D. Mochly-Rosen, T. D. Hurley
Alda-1 Is An Agonist And Chemical Chaperone For The Common Human Aldehyde Dehydrogenase 2 Variant.
Nat. Struct. Mol. Biol. V. 17 159 2010
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 19)
Info
All Hetero Components
1a: N-(1,3-BENZODIOXOL-5-YLMETHYL)-2,6... (BXBa)
1b: N-(1,3-BENZODIOXOL-5-YLMETHYL)-2,6... (BXBb)
1c: N-(1,3-BENZODIOXOL-5-YLMETHYL)-2,6... (BXBc)
1d: N-(1,3-BENZODIOXOL-5-YLMETHYL)-2,6... (BXBd)
1e: N-(1,3-BENZODIOXOL-5-YLMETHYL)-2,6... (BXBe)
1f: N-(1,3-BENZODIOXOL-5-YLMETHYL)-2,6... (BXBf)
1g: N-(1,3-BENZODIOXOL-5-YLMETHYL)-2,6... (BXBg)
1h: N-(1,3-BENZODIOXOL-5-YLMETHYL)-2,6... (BXBh)
2a: 1,2-ETHANEDIOL (EDOa)
2aa: 1,2-ETHANEDIOL (EDOaa)
2ab: 1,2-ETHANEDIOL (EDOab)
2ac: 1,2-ETHANEDIOL (EDOac)
2ad: 1,2-ETHANEDIOL (EDOad)
2ae: 1,2-ETHANEDIOL (EDOae)
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)
2z: 1,2-ETHANEDIOL (EDOz)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
3c: SODIUM ION (NAc)
3d: SODIUM ION (NAd)
3e: SODIUM ION (NAe)
3f: SODIUM ION (NAf)
3g: SODIUM ION (NAg)
3h: SODIUM ION (NAh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BXB
4
Ligand/Ion
N-(1,3-BENZODIOXOL-5-YLMETHYL)-2,6-DICHLOROBENZAMIDE
2
EDO
15
Ligand/Ion
1,2-ETHANEDIOL
3
NA
-1
Ligand/Ion
SODIUM ION
[
close Hetero Component info
]
Sites
(23, 23)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:39 , VAL A:40 , ASP A:109 , GLN A:196 , HOH A:501
BINDING SITE FOR RESIDUE NA A 601
02
AC2
SOFTWARE
ASN A:169 , CYS A:301 , SER A:302 , CYS A:303 , PHE A:465 , BXB A:1001
BINDING SITE FOR RESIDUE EDO A 701
03
AC3
SOFTWARE
ASN A:440 , PHE C:151 , ASN D:440
BINDING SITE FOR RESIDUE EDO A 702
04
AC4
SOFTWARE
LEU A:367 , CYS A:369 , GLY A:370 , HOH A:1692
BINDING SITE FOR RESIDUE EDO A 703
05
AC5
SOFTWARE
TYR A:153 , ARG A:155 , SER B:443 , PHE D:151
BINDING SITE FOR RESIDUE EDO A 704
06
AC6
SOFTWARE
ASN A:41 , THR A:44 , GLU A:46 , LEU A:108 , HOH A:1733 , HOH A:3047 , GLU D:46
BINDING SITE FOR RESIDUE EDO A 705
07
AC7
SOFTWARE
PHE A:18 , ASP A:98 , TYR A:101 , TYR A:203 , HOH A:572 , HOH A:1125 , HOH A:2611
BINDING SITE FOR RESIDUE EDO A 706
08
AC8
SOFTWARE
MET A:124 , LEU A:173 , PHE A:292 , PHE A:296 , ASP A:457 , VAL A:458 , PHE A:459 , EDO A:701
BINDING SITE FOR RESIDUE BXB A 1001
09
AC9
SOFTWARE
THR B:39 , VAL B:40 , ASP B:109 , GLN B:196 , HOH B:3389
BINDING SITE FOR RESIDUE NA B 601
10
BC1
SOFTWARE
ASN B:169 , PHE B:170 , CYS B:301 , SER B:302 , CYS B:303 , BXB B:1001
BINDING SITE FOR RESIDUE EDO B 701
11
BC2
SOFTWARE
LYS B:327 , CYS B:369 , GLY B:370 , HOH B:2081
BINDING SITE FOR RESIDUE EDO B 702
12
BC3
SOFTWARE
SER A:443 , TYR B:153 , ARG B:155 , PHE C:151
BINDING SITE FOR RESIDUE EDO B 703
13
BC4
SOFTWARE
ASN B:41 , THR B:44 , GLU B:46 , LEU B:108 , HOH B:2322
BINDING SITE FOR RESIDUE EDO B 704
14
BC5
SOFTWARE
MET B:124 , PHE B:170 , LEU B:173 , PHE B:292 , PHE B:296 , ASP B:457 , VAL B:458 , PHE B:459 , EDO B:701
BINDING SITE FOR RESIDUE BXB B 1001
15
BC6
SOFTWARE
THR C:39 , VAL C:40 , ASP C:109 , GLN C:196 , HOH C:501
BINDING SITE FOR RESIDUE NA C 601
16
BC7
SOFTWARE
ASN C:169 , CYS C:301 , SER C:302 , BXB C:1001
BINDING SITE FOR RESIDUE EDO C 701
17
BC8
SOFTWARE
PHE B:151 , TYR C:153 , ARG C:155 , HOH C:1990 , SER D:443
BINDING SITE FOR RESIDUE EDO C 702
18
BC9
SOFTWARE
ASN C:41 , THR C:44 , ILE C:48 , LEU C:108 , HOH C:2616
BINDING SITE FOR RESIDUE EDO C 703
19
CC1
SOFTWARE
MET C:124 , PHE C:170 , LEU C:173 , PHE C:292 , PHE C:296 , ASP C:457 , VAL C:458 , PHE C:459 , EDO C:701 , HOH D:2063
BINDING SITE FOR RESIDUE BXB C 1001
20
CC2
SOFTWARE
THR D:39 , VAL D:40 , ASP D:109 , GLN D:196 , HOH D:501
BINDING SITE FOR RESIDUE NA D 601
21
CC3
SOFTWARE
ASN D:169 , PHE D:170 , SER D:302 , CYS D:303 , PHE D:465 , BXB D:1001
BINDING SITE FOR RESIDUE EDO D 701
22
CC4
SOFTWARE
PHE A:151 , ASN C:440 , SER C:443 , TYR D:153 , ARG D:155
BINDING SITE FOR RESIDUE EDO D 702
23
CC5
SOFTWARE
MET D:124 , PHE D:170 , LEU D:173 , PHE D:296 , ASP D:457 , PHE D:459 , EDO D:701 , HOH D:1940
BINDING SITE FOR RESIDUE BXB D 1001
[
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 A/B/C/D, )
2: VAR_011302 (E479K, chain A/B/C/D, )
3: VAR_002248 (K487K, chain A/B/C/D, )
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
A/B/C/D
E
320
V
2
UniProt
VAR_011302
E
496
K
ALDH2_HUMAN
Polymorphism
---
A/B/C/D
E
479
K
3
UniProt
VAR_002248
E
504
K
ALDH2_HUMAN
Polymorphism
671
A/B/C/D
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 (A:267-274,B:267-274,C:267-274,D:26...)
2: ALDEHYDE_DEHYDR_CYS (A:295-306,B:295-306,C:295-306,D: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
A:267-274
B:267-274
C:267-274
D:267-274
-
-
-
-
2
ALDEHYDE_DEHYDR_CYS
PS00070
Aldehyde dehydrogenases cysteine active site.
ALDH2_HUMAN
312-323
4
A:295-306
B:295-306
C:295-306
D: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, 8)
Info
All SCOP Domains
1a: SCOP_d3inla_ (A:)
1b: SCOP_d3inlb_ (B:)
1c: SCOP_d3inlc_ (C:)
1d: SCOP_d3inld_ (D:)
1e: SCOP_d3inle_ (E:)
1f: SCOP_d3inlf_ (F:)
1g: SCOP_d3inlg_ (G:)
1h: SCOP_d3inlh_ (H:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
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
d3inla_
A:
1b
d3inlb_
B:
1c
d3inlc_
C:
1d
d3inld_
D:
1e
d3inle_
E:
1f
d3inlf_
F:
1g
d3inlg_
G:
1h
d3inlh_
H:
[
close SCOP info
]
CATH Domains
(2, 16)
Info
all CATH domains
1a: CATH_3inlA01 (A:8-270,A:461-500)
1b: CATH_3inlB01 (B:8-270,B:461-500)
1c: CATH_3inlC01 (C:8-270,C:461-500)
1d: CATH_3inlD01 (D:8-270,D:461-500)
1e: CATH_3inlE01 (E:8-270,E:461-500)
1f: CATH_3inlF01 (F:8-270,F:461-500)
1g: CATH_3inlG01 (G:8-270,G:461-500)
1h: CATH_3inlH01 (H:8-270,H:461-500)
2a: CATH_3inlA02 (A:271-460)
2b: CATH_3inlC02 (C:271-460)
2c: CATH_3inlD02 (D:271-460)
2d: CATH_3inlE02 (E:271-460)
2e: CATH_3inlF02 (F:271-460)
2f: CATH_3inlG02 (G:271-460)
2g: CATH_3inlH02 (H:271-460)
2h: CATH_3inlB02 (B:271-460)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
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
3inlA01
A:8-270,A:461-500
1b
3inlB01
B:8-270,B:461-500
1c
3inlC01
C:8-270,C:461-500
1d
3inlD01
D:8-270,D:461-500
1e
3inlE01
E:8-270,E:461-500
1f
3inlF01
F:8-270,F:461-500
1g
3inlG01
G:8-270,G:461-500
1h
3inlH01
H:8-270,H:461-500
Topology
:
Aldehyde Dehydrogenase; Chain A, domain 2
(89)
Homologous Superfamily
:
Aldehyde Dehydrogenase; Chain A, domain 2
(89)
Human (Homo sapiens)
(22)
2a
3inlA02
A:271-460
2b
3inlC02
C:271-460
2c
3inlD02
D:271-460
2d
3inlE02
E:271-460
2e
3inlF02
F:271-460
2f
3inlG02
G:271-460
2g
3inlH02
H:271-460
2h
3inlB02
B:271-460
[
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
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(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)
[
close Script example commands
]
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") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (690 KB)
Header - Asym.Unit
Biol.Unit 1 (344 KB)
Header - Biol.Unit 1
Biol.Unit 2 (347 KB)
Header - Biol.Unit 2
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
3INL
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help