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...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
1U8V
Asym. Unit
Info
Asym.Unit (367 KB)
Biol.Unit 1 (360 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF 4-HYDROXYBUTYRYL-COA DEHYDRATASE FROM CLOSTRIDIUM AMINOBUTYRICUM: RADICAL CATALYSIS INVOLVING A [4FE-4S] CLUSTER AND FLAVIN
Authors
:
B. M. Martins, H. Dobbek, I. Cinkaya, W. Buckel, A. Messerschmidt
Date
:
07 Aug 04 (Deposition) - 21 Dec 04 (Release) - 24 Mar 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Alfa-Helixes, Beta-Strands, Lyase, Isomerase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. M. Martins, H. Dobbek, I. Cinkaya, W. Buckel, A. Messerschmidt
Crystal Structure Of 4-Hydroxybutyryl-Coa Dehydratase: Radical Catalysis Involving A [4Fe-4S] Cluster And Flavin.
Proc. Natl. Acad. Sci. Usa V. 101 15645 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 8)
Info
All Hetero Components
1a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
1b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
1c: FLAVIN-ADENINE DINUCLEOTIDE (FADc)
1d: FLAVIN-ADENINE DINUCLEOTIDE (FADd)
2a: IRON/SULFUR CLUSTER (SF4a)
2b: IRON/SULFUR CLUSTER (SF4b)
2c: IRON/SULFUR CLUSTER (SF4c)
2d: IRON/SULFUR CLUSTER (SF4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FAD
4
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
2
SF4
4
Ligand/Ion
IRON/SULFUR CLUSTER
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS A:99 , PHE A:100 , GLN A:101 , CYS A:103 , HIS A:292 , SER A:295 , CYS A:299
BINDING SITE FOR RESIDUE SF4 A 491
2
AC2
SOFTWARE
MET A:149 , THR A:150 , LYS A:153 , ARG A:156 , HIS A:188 , GLN A:189 , THR A:190 , GLU A:455 , HIS A:458 , SER A:462 , HOH A:6207 , HOH A:6366 , HOH A:6398 , HOH A:6473 , HOH A:6995 , HOH A:8186 , HOH A:8628 , ALA B:323 , HIS B:325 , ASP B:386 , ILE B:387 , GLY B:389 , GLY B:390 , HOH B:6027 , HOH B:6260 , HOH B:6293 , HOH B:6403
BINDING SITE FOR RESIDUE FAD A 492
3
AC3
SOFTWARE
CYS B:99 , PHE B:100 , CYS B:103 , HIS B:292 , SER B:295 , CYS B:299 , GLU B:455 , HOH B:8832
BINDING SITE FOR RESIDUE SF4 B 491
4
AC4
SOFTWARE
ALA A:323 , HIS A:325 , ASP A:386 , ILE A:387 , GLY A:389 , GLY A:390 , HOH A:6006 , HOH A:6016 , HOH A:6238 , MET B:149 , THR B:150 , LYS B:153 , ARG B:156 , HIS B:188 , GLN B:189 , THR B:190 , GLU B:455 , HIS B:458 , SER B:462 , HOH B:6179 , HOH B:6252 , HOH B:6294 , HOH B:6354 , HOH B:6433 , HOH B:6715 , HOH B:6758 , HOH B:6829 , HOH B:7008 , HOH B:7861 , HOH B:8523
BINDING SITE FOR RESIDUE FAD B 492
5
AC5
SOFTWARE
CYS C:99 , PHE C:100 , GLN C:101 , CYS C:103 , HIS C:292 , SER C:295 , CYS C:299 , GLU C:455
BINDING SITE FOR RESIDUE SF4 C 491
6
AC6
SOFTWARE
MET C:149 , THR C:150 , LYS C:153 , ARG C:156 , HIS C:188 , GLN C:189 , THR C:190 , GLU C:455 , HIS C:458 , SER C:462 , HOH C:6046 , HOH C:6093 , HOH C:6168 , HOH C:6242 , HOH C:6421 , HOH C:6773 , HOH C:6944 , HOH C:7193 , HOH C:7264 , HOH C:7559 , HOH C:7597 , ALA D:323 , HIS D:325 , ASP D:386 , ILE D:387 , GLY D:389 , GLY D:390 , HOH D:6132 , HOH D:6159 , HOH D:6175
BINDING SITE FOR RESIDUE FAD C 492
7
AC7
SOFTWARE
CYS D:99 , PHE D:100 , GLN D:101 , CYS D:103 , HIS D:292 , SER D:295 , CYS D:299 , GLU D:455
BINDING SITE FOR RESIDUE SF4 D 491
8
AC8
SOFTWARE
ALA C:323 , HIS C:325 , ASP C:386 , ILE C:387 , GLY C:389 , GLY C:390 , HOH C:6037 , HOH C:6170 , HOH C:6176 , MET D:149 , THR D:150 , LYS D:153 , ARG D:156 , HIS D:188 , GLN D:189 , THR D:190 , GLU D:455 , HIS D:458 , HOH D:6169 , HOH D:6171 , HOH D:6314 , HOH D:6361 , HOH D:6381 , HOH D:6508 , HOH D:6641 , HOH D:7196 , HOH D:8235
BINDING SITE FOR RESIDUE FAD D 492
[
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
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1u8va1 (A:276-490)
1b: SCOP_d1u8vb1 (B:276-490)
1c: SCOP_d1u8vc1 (C:276-490)
1d: SCOP_d1u8vd1 (D:276-490)
2a: SCOP_d1u8va2 (A:1-275)
2b: SCOP_d1u8vb2 (B:1-275)
2c: SCOP_d1u8vc2 (C:1-275)
2d: SCOP_d1u8vd2 (D:1-275)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Bromodomain-like
(339)
Superfamily
:
Acyl-CoA dehydrogenase C-terminal domain-like
(61)
Family
:
Medium chain acyl-CoA dehydrogenase-like, C-terminal domain
(29)
Protein domain
:
4-hydroxybutyryl-CoA dehydratase AbfD, C-terminal domain
(1)
Clostridium aminobutyricum [TaxId: 33953]
(1)
1a
d1u8va1
A:276-490
1b
d1u8vb1
B:276-490
1c
d1u8vc1
C:276-490
1d
d1u8vd1
D:276-490
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
Acyl-CoA dehydrogenase NM domain-like
(61)
Superfamily
:
Acyl-CoA dehydrogenase NM domain-like
(61)
Family
:
Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains
(32)
Protein domain
:
4-hydroxybutyryl-CoA dehydratase AbfD, NM domains
(1)
Clostridium aminobutyricum [TaxId: 33953]
(1)
2a
d1u8va2
A:1-275
2b
d1u8vb2
B:1-275
2c
d1u8vc2
C:1-275
2d
d1u8vd2
D:1-275
[
close SCOP info
]
CATH Domains
(3, 12)
Info
all CATH domains
1a: CATH_1u8vA01 (A:1-143)
1b: CATH_1u8vB01 (B:1-143)
1c: CATH_1u8vC01 (C:1-143)
1d: CATH_1u8vD01 (D:1-143)
2a: CATH_1u8vB03 (B:278-490)
2b: CATH_1u8vA03 (A:277-490)
2c: CATH_1u8vC03 (C:277-490)
2d: CATH_1u8vD03 (D:277-490)
3a: CATH_1u8vA02 (A:144-276)
3b: CATH_1u8vC02 (C:144-276)
3c: CATH_1u8vD02 (D:144-276)
3d: CATH_1u8vB02 (B:144-277)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
4-hydroxybutyryl-coa dehydratase, domain 1
(1)
Homologous Superfamily
:
4-hydroxybutyryl-coa dehydratase, domain 1
(1)
Clostridium aminobutyricum. Organism_taxid: 33953
(1)
1a
1u8vA01
A:1-143
1b
1u8vB01
B:1-143
1c
1u8vC01
C:1-143
1d
1u8vD01
D:1-143
Architecture
:
Up-down Bundle
(3216)
Topology
:
Butyryl-CoA Dehydrogenase, subunit A; domain 3
(76)
Homologous Superfamily
:
Butyryl-CoA Dehydrogenase, subunit A, domain 3
(37)
Clostridium aminobutyricum. Organism_taxid: 33953
(1)
2a
1u8vB03
B:278-490
2b
1u8vA03
A:277-490
2c
1u8vC03
C:277-490
2d
1u8vD03
D:277-490
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Butyryl-CoA Dehydrogenase, subunit A; domain 2
(35)
Homologous Superfamily
:
Butyryl-CoA Dehydrogenase, subunit A, domain 2
(35)
Clostridium aminobutyricum. Organism_taxid: 33953
(1)
3a
1u8vA02
A:144-276
3b
1u8vC02
C:144-276
3c
1u8vD02
D:144-276
3d
1u8vB02
B:144-277
[
close CATH info
]
Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_HpaB_1u8vD01 (D:279-489)
1b: PFAM_HpaB_1u8vD02 (D:279-489)
1c: PFAM_HpaB_1u8vD03 (D:279-489)
1d: PFAM_HpaB_1u8vD04 (D:279-489)
2a: PFAM_HpaB_N_1u8vD05 (D:4-274)
2b: PFAM_HpaB_N_1u8vD06 (D:4-274)
2c: PFAM_HpaB_N_1u8vD07 (D:4-274)
2d: PFAM_HpaB_N_1u8vD08 (D:4-274)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Acyl-CoA_dh
(32)
Family
:
HpaB
(7)
Clostridium aminobutyricum
(1)
1a
HpaB-1u8vD01
D:279-489
1b
HpaB-1u8vD02
D:279-489
1c
HpaB-1u8vD03
D:279-489
1d
HpaB-1u8vD04
D:279-489
Clan
:
no clan defined [family: HpaB_N]
(7)
Family
:
HpaB_N
(7)
Clostridium aminobutyricum
(1)
2a
HpaB_N-1u8vD05
D:4-274
2b
HpaB_N-1u8vD06
D:4-274
2c
HpaB_N-1u8vD07
D:4-274
2d
HpaB_N-1u8vD08
D:4-274
[
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 (367 KB)
Header - Asym.Unit
Biol.Unit 1 (360 KB)
Header - Biol.Unit 1
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
1U8V
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help