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.
1H0H
Biol. Unit 2
Info
Asym.Unit (435 KB)
Biol.Unit 1 (218 KB)
Biol.Unit 2 (214 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
TUNGSTEN CONTAINING FORMATE DEHYDROGENASE FROM DESULFOVIBRIO GIGAS
Authors
:
H. C. A. Raaijmakers
Date
:
19 Jun 02 (Deposition) - 20 Feb 03 (Release) - 28 Jun 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,K,L
Biol. Unit 1: A,B (1x)
Biol. Unit 2: K,L (1x)
Keywords
:
Electron Transport, Tungsten Selenium Formate Dehydrogenase, Selenocysteine, Molybdopterin, Mgd, Iron-Sulphur Cluster, Periplasmic
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. C. A. Raaijmakers, S. Macieira, J. Dias, S. Teixeira, S. Bursakov, R. Huber, J. Moura, I. Moura, M. Romao
Gene Sequence And The 1. 8 A Crystal Structure Of The Tungsten-Containing Formate Dehydrogenase From Desulfovibri Gigas
Structure V. 10 1261 2002
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(5, 8)
Info
All Hetero Components
1a: GUANYLATE-O'-PHOSPHORIC ACID MONO-... (2MDa)
1b: GUANYLATE-O'-PHOSPHORIC ACID MONO-... (2MDb)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
3a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
3b: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEb)
4a: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (MGDa)
4b: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (MGDb)
5a: (SECa)
5b: (SECb)
6a: IRON/SULFUR CLUSTER (SF4a)
6b: IRON/SULFUR CLUSTER (SF4b)
6c: IRON/SULFUR CLUSTER (SF4c)
6d: IRON/SULFUR CLUSTER (SF4d)
6e: IRON/SULFUR CLUSTER (SF4e)
6f: IRON/SULFUR CLUSTER (SF4f)
6g: IRON/SULFUR CLUSTER (SF4g)
6h: IRON/SULFUR CLUSTER (SF4h)
7a: UNKNOWN ATOM OR ION (UNXa)
7b: UNKNOWN ATOM OR ION (UNXb)
8a: TUNGSTEN ION (Wa)
8b: TUNGSTEN ION (Wb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
2MD
1
Ligand/Ion
GUANYLATE-O'-PHOSPHORIC ACID MONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,5,6,7,8A,9,10,10A-OCTAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL) ESTER
2
CA
-1
Ligand/Ion
CALCIUM ION
3
EPE
1
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4
MGD
1
Ligand/Ion
2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINEDINUCLEOTIDE
5
SEC
-1
Mod. Amino Acid
6
SF4
4
Ligand/Ion
IRON/SULFUR CLUSTER
7
UNX
1
Ligand/Ion
UNKNOWN ATOM OR ION
8
W
-1
Ligand/Ion
TUNGSTEN ION
[
close Hetero Component info
]
Sites
(10, 10)
Info
All Sites
01: AC2 (SOFTWARE)
02: AC4 (SOFTWARE)
03: BC4 (SOFTWARE)
04: BC5 (SOFTWARE)
05: BC6 (SOFTWARE)
06: BC7 (SOFTWARE)
07: BC8 (SOFTWARE)
08: BC9 (SOFTWARE)
09: CC1 (SOFTWARE)
10: CC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC2
SOFTWARE
THR K:358 , LYS K:360 , LYS K:363 , LEU K:393 , GLY K:394 , ASN K:395 , HOH K:2287
BINDING SITE FOR RESIDUE CA K 1100
02
AC4
SOFTWARE
SEC K:158 , 2MD K:1001 , MGD K:1002 , UNX K:1003
BINDING SITE FOR RESIDUE W K 1000
03
BC4
SOFTWARE
ALA K:130 , GLN K:154 , ILE K:157 , SEC K:158 , MET K:371 , GLU K:409 , GLY K:516 , GLN K:517 , ASN K:518 , SER K:522 , VAL K:542 , ASN K:543 , ILE K:544 , CYS K:572 , ALA K:573 , LYS K:578 , ASP K:605 , THR K:854 , ARG K:856 , GLN K:862 , THR K:863 , LEU K:865 , MET K:866 , TRP K:936 , ASN K:951 , THR K:967 , W K:1000 , MGD K:1002 , UNX K:1003 , HOH K:2561 , HOH K:2611 , HOH K:2618
BINDING SITE FOR RESIDUE 2MD K 1001
04
BC5
SOFTWARE
LYS K:56 , SEC K:158 , GLY K:192 , SER K:193 , ASN K:194 , GLU K:197 , ASN K:198 , VAL K:219 , ASP K:220 , PRO K:221 , ARG K:222 , SER K:238 , GLY K:239 , ASP K:241 , ALA K:370 , MET K:371 , TRP K:373 , GLY K:408 , TYR K:855 , ARG K:856 , VAL K:857 , THR K:858 , HIS K:860 , TRP K:861 , GLN K:862 , HIS K:937 , LYS K:968 , W K:1000 , 2MD K:1001 , UNX K:1003 , HOH K:2162 , HOH K:2276 , HOH K:2612 , HOH K:2619 , HOH K:2620
BINDING SITE FOR RESIDUE MGD K 1002
05
BC6
SOFTWARE
SEC K:158 , GLU K:409 , VAL K:412 , W K:1000 , 2MD K:1001 , MGD K:1002
BINDING SITE FOR RESIDUE UNX K 1003
06
BC7
SOFTWARE
CYS K:17 , TYR K:19 , CYS K:20 , GLY K:23 , CYS K:24 , LEU K:53 , CYS K:54 , LYS K:56 , GLY K:57 , PRO K:200 , ILE K:201
BINDING SITE FOR RESIDUE SF4 K 1010
07
BC8
SOFTWARE
HOH K:2623 , PRO L:42 , ASP L:43 , ASP L:123
BINDING SITE FOR RESIDUE EPE K 1200
08
BC9
SOFTWARE
CYS L:11 , THR L:12 , ALA L:13 , CYS L:14 , ARG L:15 , CYS L:17 , CYS L:156 , THR L:158 , MET L:161
BINDING SITE FOR RESIDUE SF4 L 1011
09
CC1
SOFTWARE
PHE L:4 , CYS L:21 , HIS L:25 , LYS L:50 , GLN L:71 , CYS L:137 , ASP L:138 , MET L:139 , CYS L:140 , PRO L:150 , CYS L:152
BINDING SITE FOR RESIDUE SF4 L 1012
10
CC2
SOFTWARE
CYS L:72 , ARG L:73 , CYS L:75 , PRO L:79 , CYS L:80 , CYS L:120 , TYR L:122 , PRO L:125 , LYS L:136
BINDING SITE FOR RESIDUE SF4 L 1013
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 3)
Info
All PROSITE Patterns/Profiles
1: 4FE4S_MOW_BIS_MGD (K:10-68)
2: MOLYBDOPTERIN_PROK_1 (K:15-33)
3: MOLYBDOPTERIN_PROK_3 (K:889-916)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
4FE4S_MOW_BIS_MGD
PS51669
Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile.
FDHA_DESGI
45-103
1
-
K:10-68
2
MOLYBDOPTERIN_PROK_1
PS00551
Prokaryotic molybdopterin oxidoreductases signature 1.
FDHA_DESGI
50-68
1
-
K:15-33
3
MOLYBDOPTERIN_PROK_3
PS00932
Prokaryotic molybdopterin oxidoreductases signature 3.
FDHA_DESGI
924-951
1
-
K:889-916
[
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
(3, 6)
Info
All SCOP Domains
1a: SCOP_d1h0ha1 (A:813-977)
1b: SCOP_d1h0hk1 (K:813-977)
2a: SCOP_d1h0hb_ (B:)
2b: SCOP_d1h0hl_ (L:)
3a: SCOP_d1h0ha2 (A:1-812)
3b: SCOP_d1h0hk2 (K:1-812)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Double psi beta-barrel
(111)
Superfamily
:
ADC-like
(88)
Family
:
Formate dehydrogenase/DMSO reductase, C-terminal domain
(41)
Protein domain
:
Tungsten containing formate dehydrogenase, large subunit
(1)
Desulfovibrio gigas [TaxId: 879]
(1)
1a
d1h0ha1
A:813-977
1b
d1h0hk1
K:813-977
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
4Fe-4S ferredoxins
(143)
Family
:
Ferredoxin domains from multidomain proteins
(69)
Protein domain
:
Tungsten containing formate dehydrogenase, small subunit
(1)
Desulfovibrio gigas [TaxId: 879]
(1)
2a
d1h0hb_
B:
2b
d1h0hl_
L:
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Formate dehydrogenase/DMSO reductase, domains 1-3
(53)
Superfamily
:
Formate dehydrogenase/DMSO reductase, domains 1-3
(53)
Family
:
Formate dehydrogenase/DMSO reductase, domains 1-3
(53)
Protein domain
:
Tungsten containing formate dehydrogenase, large subunit
(1)
Desulfovibrio gigas [TaxId: 879]
(1)
3a
d1h0ha2
A:1-812
3b
d1h0hk2
K:1-812
[
close SCOP info
]
CATH Domains
(4, 10)
Info
all CATH domains
1a: CATH_1h0hB02 (B:74-137)
1b: CATH_1h0hL02 (L:74-137)
1c: CATH_1h0hB01 (B:1-73,B:138-214)
1d: CATH_1h0hL01 (L:1-73,L:138-214)
2a: CATH_1h0hA03 (A:157-268,A:321-410,A:735-801)
2b: CATH_1h0hK03 (K:157-268,K:321-410,K:735-801)
3a: CATH_1h0hA02 (A:69-156,A:490-640)
3b: CATH_1h0hK02 (K:69-156,K:490-640)
4a: CATH_1h0hA04 (A:802-977)
4b: CATH_1h0hK04 (K:802-977)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.20, no name defined]
(120)
Desulfovibrio gigas. Organism_taxid: 879. Strain: ncib 9332.
(1)
1a
1h0hB02
B:74-137
1b
1h0hL02
L:74-137
1c
1h0hB01
B:1-73,B:138-214
1d
1h0hL01
L:1-73,L:138-214
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Dimethylsulfoxide Reductase; domain 2
(37)
Homologous Superfamily
:
Dimethylsulfoxide Reductase, domain 2
(37)
Desulfovibrio gigas. Organism_taxid: 879. Strain: ncib 9332.
(1)
2a
1h0hA03
A:157-268,A:321-410,A:735-801
2b
1h0hK03
K:157-268,K:321-410,K:735-801
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.740, no name defined]
(37)
Desulfovibrio gigas. Organism_taxid: 879. Strain: ncib 9332.
(1)
3a
1h0hA02
A:69-156,A:490-640
3b
1h0hK02
K:69-156,K:490-640
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Barwin-like endoglucanases
(75)
Homologous Superfamily
:
[code=2.40.40.20, no name defined]
(63)
Desulfovibrio gigas. Organism_taxid: 879. Strain: ncib 9332.
(1)
4a
1h0hA04
A:802-977
4b
1h0hK04
K:802-977
[
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 K
Chain L
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 (435 KB)
Header - Asym.Unit
Biol.Unit 1 (218 KB)
Header - Biol.Unit 1
Biol.Unit 2 (214 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
1H0H
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
