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1N63
Asym. Unit
Info
Asym.Unit (901 KB)
Biol.Unit 1 (889 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE CU,MO-CO DEHYDROGENASE (CODH); CARBON MONOXIDE REDUCED STATE
Authors
:
H. Dobbek, L. Gremer, R. Kiefersauer, R. Huber, O. Meyer
Date
:
08 Nov 02 (Deposition) - 18 Dec 02 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.21
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Codh, Molybdenum, Molybdopterin, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Dobbek, L. Gremer, R. Kiefersauer, R. Huber, O. Meyer
Catalysis At A Dinuclear [Cusmo(=O)Oh] Cluster In A Co Dehydrogenase Resolved At 1. 1-A Resolution
Proc. Natl. Acad. Sci. Usa V. 99 15971 2002
[
close entry info
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Hetero Components
(5, 11)
Info
All Hetero Components
1a: CU(I)-S-MO(IV)(=O)OH CLUSTER (CUNa)
1b: CU(I)-S-MO(IV)(=O)OH CLUSTER (CUNb)
2a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
2b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
3a: FE2/S2 (INORGANIC) CLUSTER (FESa)
3b: FE2/S2 (INORGANIC) CLUSTER (FESb)
3c: FE2/S2 (INORGANIC) CLUSTER (FESc)
3d: FE2/S2 (INORGANIC) CLUSTER (FESd)
4a: PTERIN CYTOSINE DINUCLEOTIDE (MCNa)
4b: PTERIN CYTOSINE DINUCLEOTIDE (MCNb)
5a: PHOSPHATE ION (PO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CUN
2
Ligand/Ion
CU(I)-S-MO(IV)(=O)OH CLUSTER
2
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
3
FES
4
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
4
MCN
2
Ligand/Ion
PTERIN CYTOSINE DINUCLEOTIDE
5
PO4
1
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
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Sites
(11, 11)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:5 , HOH A:3982 , HOH A:4026 , HOH A:4076 , HOH A:4080
BINDING SITE FOR RESIDUE PO4 A 3001
02
AC2
SOFTWARE
GLN A:101 , CYS A:102 , GLY A:103 , CYS A:105 , CYS A:137 , ARG A:138 , CYS A:139
BINDING SITE FOR RESIDUE FES A 3907
03
AC3
SOFTWARE
GLY A:41 , CYS A:42 , SER A:45 , HIS A:46 , CYS A:47 , GLY A:48 , CYS A:50 , CYS A:62
BINDING SITE FOR RESIDUE FES A 3908
04
AC4
SOFTWARE
GLN B:240 , GLY B:272 , ALA B:385 , TYR B:386 , ARG B:387 , CYS B:388 , SER B:389 , TYR B:568 , GLY B:569 , GLU B:763 , MCN B:3920 , HOH B:4304
BINDING SITE FOR RESIDUE CUN B 3921
05
AC5
SOFTWARE
GLN A:101 , CYS A:139 , GLY B:270 , PHE B:271 , ARG B:387 , GLN B:528 , GLY B:529 , GLN B:530 , HIS B:532 , THR B:535 , THR B:567 , TYR B:568 , GLY B:569 , SER B:570 , ARG B:571 , SER B:572 , THR B:573 , CYS B:686 , THR B:688 , ILE B:690 , ASN B:691 , ILE B:694 , ILE B:695 , GLN B:698 , LYS B:759 , GLY B:760 , VAL B:761 , GLY B:762 , GLU B:763 , CUN B:3921 , HOH B:4001
BINDING SITE FOR RESIDUE MCN B 3920
06
AC6
SOFTWARE
GLN D:101 , CYS D:102 , GLY D:103 , CYS D:105 , CYS D:137 , ARG D:138 , CYS D:139
BINDING SITE FOR RESIDUE FES D 4907
07
AC7
SOFTWARE
GLY D:41 , CYS D:42 , SER D:45 , HIS D:46 , CYS D:47 , GLY D:48 , CYS D:50 , CYS D:62
BINDING SITE FOR RESIDUE FES D 4908
08
AC8
SOFTWARE
GLN E:240 , GLY E:272 , ALA E:385 , TYR E:386 , ARG E:387 , CYS E:388 , SER E:389 , TYR E:568 , GLY E:569 , GLU E:763 , MCN E:4920 , HOH E:5295
BINDING SITE FOR RESIDUE CUN E 4921
09
AC9
SOFTWARE
GLN D:101 , CYS D:139 , GLY E:270 , PHE E:271 , ARG E:387 , GLN E:528 , GLY E:529 , GLN E:530 , HIS E:532 , THR E:535 , THR E:567 , TYR E:568 , GLY E:569 , SER E:570 , ARG E:571 , SER E:572 , THR E:573 , CYS E:686 , THR E:688 , ILE E:690 , ASN E:691 , ILE E:694 , ILE E:695 , GLN E:698 , LYS E:759 , GLY E:760 , VAL E:761 , GLY E:762 , GLU E:763 , CUN E:4921 , HOH E:5037
BINDING SITE FOR RESIDUE MCN E 4920
10
BC1
SOFTWARE
SER D:45 , HIS D:46 , ARG F:29 , PRO F:30 , ALA F:32 , GLY F:33 , GLY F:34 , HIS F:35 , SER F:36 , LEU F:37 , ILE F:101 , ALA F:102 , ILE F:106 , GLY F:110 , THR F:111 , GLY F:114 , ASN F:115 , ASN F:118 , ASN F:123 , ASP F:124 , LEU F:167 , LYS F:185 , GLY F:191 , ASP F:192 , TYR F:193 , HOH F:4938 , HOH F:4942 , HOH F:4981 , HOH F:5002 , HOH F:5056 , HOH F:5131 , HOH F:5211
BINDING SITE FOR RESIDUE FAD F 4931
11
BC2
SOFTWARE
SER A:45 , HIS A:46 , ARG C:29 , PRO C:30 , ALA C:32 , GLY C:33 , GLY C:34 , HIS C:35 , SER C:36 , LEU C:37 , ALA C:74 , ILE C:101 , ALA C:102 , ILE C:106 , GLY C:110 , THR C:111 , GLY C:114 , ASN C:115 , ASN C:118 , ASN C:123 , ASP C:124 , ILE C:161 , LEU C:166 , LEU C:167 , LYS C:185 , GLY C:191 , TYR C:193 , HOH C:3938 , HOH C:3950 , HOH C:4029 , HOH C:4056 , HOH C:4072 , HOH C:4266
BINDING SITE FOR RESIDUE FAD C 3932
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: FAD_PCMH (C:1-177,F:1-177)
2: 2FE2S_FER_2 (A:4-80,D:4-80)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FAD_PCMH
PS51387
PCMH-type FAD-binding domain profile.
DCMM_OLICO
1-177
2
C:1-177
F:1-177
2
2FE2S_FER_2
PS51085
2Fe-2S ferredoxin-type iron-sulfur binding domain profile.
DCMS_OLICO
4-80
2
A:4-80
D:4-80
[
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Exons
(0, 0)
Info
All Exons
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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
(6, 12)
Info
All SCOP Domains
1a: SCOP_d1n63a1 (A:82-162)
1b: SCOP_d1n63d1 (D:82-160)
2a: SCOP_d1n63b1 (B:5-146)
2b: SCOP_d1n63e1 (E:15-146)
3a: SCOP_d1n63a2 (A:3-81)
3b: SCOP_d1n63d2 (D:3-81)
4a: SCOP_d1n63c1 (C:178-287)
4b: SCOP_d1n63f1 (F:178-286)
5a: SCOP_d1n63c2 (C:1-177)
5b: SCOP_d1n63f2 (F:1-177)
6a: SCOP_d1n63b2 (B:147-809)
6b: SCOP_d1n63e2 (E:147-809)
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Classes
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)
(
)
Folds
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)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
CO dehydrogenase ISP C-domain like
(45)
Superfamily
:
CO dehydrogenase ISP C-domain like
(45)
Family
:
CO dehydrogenase ISP C-domain like
(42)
Protein domain
:
Carbon monoxide (CO) dehydrogenase iron-sulfur protein, C-domain
(8)
Oligotropha carboxidovorans, formerly Pseudomonas carboxydovorans [TaxId: 40137]
(6)
1a
d1n63a1
A:82-162
1b
d1n63d1
D:82-160
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
alpha/beta-Hammerhead
(191)
Superfamily
:
CO dehydrogenase molybdoprotein N-domain-like
(44)
Family
:
CO dehydrogenase molybdoprotein N-domain-like
(34)
Protein domain
:
Carbon monoxide (CO) dehydrogenase molybdoprotein, N-domain
(7)
Oligotropha carboxidovorans, formerly Pseudomonas carboxydovorans [TaxId: 40137]
(5)
2a
d1n63b1
B:5-146
2b
d1n63e1
E:15-146
Fold
:
beta-Grasp (ubiquitin-like)
(1032)
Superfamily
:
2Fe-2S ferredoxin-like
(174)
Family
:
2Fe-2S ferredoxin domains from multidomain proteins
(82)
Protein domain
:
Carbone monoxide (CO) dehydrogenase iron-sulfur protein, N-domain
(8)
Oligotropha carboxidovorans, formerly Pseudomonas carboxydovorans [TaxId: 40137]
(6)
3a
d1n63a2
A:3-81
3b
d1n63d2
D:3-81
Fold
:
CO dehydrogenase flavoprotein C-domain-like
(111)
Superfamily
:
CO dehydrogenase flavoprotein C-terminal domain-like
(35)
Family
:
CO dehydrogenase flavoprotein C-terminal domain-like
(23)
Protein domain
:
Carbon monoxide (CO) dehydrogenase flavoprotein, C-terminal domain
(8)
Oligotropha carboxidovorans, formerly Pseudomonas carboxydovorans [TaxId: 40137]
(6)
4a
d1n63c1
C:178-287
4b
d1n63f1
F:178-286
Fold
:
FAD-binding/transporter-associated domain-like
(99)
Superfamily
:
FAD-binding/transporter-associated domain-like
(99)
Family
:
CO dehydrogenase flavoprotein N-terminal domain-like
(33)
Protein domain
:
Carbon monoxide (CO) dehydrogenase flavoprotein, N-terminal domain
(8)
Oligotropha carboxidovorans, formerly Pseudomonas carboxydovorans [TaxId: 40137]
(6)
5a
d1n63c2
C:1-177
5b
d1n63f2
F:1-177
Fold
:
Molybdenum cofactor-binding domain
(44)
Superfamily
:
Molybdenum cofactor-binding domain
(44)
Family
:
Molybdenum cofactor-binding domain
(44)
Protein domain
:
Carbon monoxide (CO) dehydrogenase molybdoprotein
(7)
Oligotropha carboxidovorans, formerly Pseudomonas carboxydovorans [TaxId: 40137]
(5)
6a
d1n63b2
B:147-809
6b
d1n63e2
E:147-809
[
close SCOP info
]
CATH Domains
(7, 20)
Info
all CATH domains
1a: CATH_1n63B03 (B:490-655)
1b: CATH_1n63B02 (B:145-212,B:310-386)
1c: CATH_1n63E02 (E:145-212,E:310-386)
1d: CATH_1n63B05 (B:213-309)
1e: CATH_1n63E05 (E:213-309)
1f: CATH_1n63B04 (B:390-489,B:656-809)
1g: CATH_1n63E04 (E:390-489,E:656-809)
1h: CATH_1n63E03 (E:490-655)
2a: CATH_1n63C02 (C:180-284)
2b: CATH_1n63F02 (F:180-284)
3a: CATH_1n63C01 (C:1-54)
3b: CATH_1n63F01 (F:1-54)
4a: CATH_1n63C03 (C:60-174)
4b: CATH_1n63F03 (F:60-174)
5a: CATH_1n63E01 (E:15-144)
5b: CATH_1n63B01 (B:10-144)
6a: CATH_1n63A01 (A:3-79)
6b: CATH_1n63D01 (D:3-79)
7a: CATH_1n63A02 (A:80-161)
7b: CATH_1n63D02 (D:80-160)
View:
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Classes
(
)
(
)
Architectures
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)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Aldehyde Oxidoreductase; domain 4
(20)
Homologous Superfamily
:
Aldehyde Oxidoreductase; domain 4
(20)
Oligotropha carboxidovorans om5. Organism_taxid: 504832. Strain: om5.Oligotropha carboxidovorans om5. Organism_taxid: 504832. Strain: om5.
(6)
1a
1n63B03
B:490-655
1b
1n63B02
B:145-212,B:310-386
1c
1n63E02
E:145-212,E:310-386
1d
1n63B05
B:213-309
1e
1n63E05
E:213-309
1f
1n63B04
B:390-489,B:656-809
1g
1n63E04
E:390-489,E:656-809
1h
1n63E03
E:490-655
Topology
:
Enolase-like; domain 1
(252)
Homologous Superfamily
:
[code=3.30.390.50, no name defined]
(22)
Oligotropha carboxidovorans om5. Organism_taxid: 504832. Strain: om5.Oligotropha carboxidovorans om5. Organism_taxid: 504832. Strain: om5.
(6)
2a
1n63C02
C:180-284
2b
1n63F02
F:180-284
Topology
:
Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
(50)
Homologous Superfamily
:
Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2
(50)
Oligotropha carboxidovorans om5. Organism_taxid: 504832. Strain: om5.Oligotropha carboxidovorans om5. Organism_taxid: 504832. Strain: om5.
(6)
3a
1n63C01
C:1-54
3b
1n63F01
F:1-54
Topology
:
Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
(63)
Homologous Superfamily
:
[code=3.30.465.10, no name defined]
(63)
Oligotropha carboxidovorans om5. Organism_taxid: 504832. Strain: om5.Oligotropha carboxidovorans om5. Organism_taxid: 504832. Strain: om5.
(6)
4a
1n63C03
C:60-174
4b
1n63F03
F:60-174
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Aldehyde Oxidoreductase; domain 3
(111)
Homologous Superfamily
:
[code=3.90.1170.50, no name defined]
(20)
Oligotropha carboxidovorans om5. Organism_taxid: 504832. Strain: om5.Oligotropha carboxidovorans om5. Organism_taxid: 504832. Strain: om5.
(6)
5a
1n63E01
E:15-144
5b
1n63B01
B:10-144
Architecture
:
Roll
(3276)
Topology
:
Ubiquitin-like (UB roll)
(674)
Homologous Superfamily
:
[code=3.10.20.30, no name defined]
(153)
Oligotropha carboxidovorans om5. Organism_taxid: 504832. Strain: om5.Oligotropha carboxidovorans om5. Organism_taxid: 504832. Strain: om5.
(6)
6a
1n63A01
A:3-79
6b
1n63D01
D:3-79
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
DNA polymerase; domain 1
(617)
Homologous Superfamily
:
[code=1.10.150.120, no name defined]
(29)
Oligotropha carboxidovorans om5. Organism_taxid: 504832. Strain: om5.Oligotropha carboxidovorans om5. Organism_taxid: 504832. Strain: om5.
(6)
7a
1n63A02
A:80-161
7b
1n63D02
D:80-160
[
close CATH info
]
Pfam Domains
(6, 12)
Info
all PFAM domains
1a: PFAM_FAD_binding_5_1n63F01 (F:4-175)
1b: PFAM_FAD_binding_5_1n63F02 (F:4-175)
2a: PFAM_Fer2_1n63D01 (D:8-75)
2b: PFAM_Fer2_1n63D02 (D:8-75)
3a: PFAM_Fer2_2_1n63D03 (D:76-151)
3b: PFAM_Fer2_2_1n63D04 (D:76-151)
4a: PFAM_Ald_Xan_dh_C2_1n63E01 (E:153-740)
4b: PFAM_Ald_Xan_dh_C2_1n63E02 (E:153-740)
5a: PFAM_Ald_Xan_dh_C_1n63E03 (E:35-144)
5b: PFAM_Ald_Xan_dh_C_1n63E04 (E:35-144)
6a: PFAM_CO_deh_flav_C_1n63F03 (F:181-282)
6b: PFAM_CO_deh_flav_C_1n63F04 (F:181-282)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
FAD_PCMH
(53)
Family
:
FAD_binding_5
(22)
Oligotropha carboxidovorans (strain ATCC 49405 / DSM 1227 / OM5)
(6)
1a
FAD_binding_5-1n63F01
F:4-175
1b
FAD_binding_5-1n63F02
F:4-175
Clan
:
Fer2
(69)
Family
:
Fer2
(60)
Oligotropha carboxidovorans (strain ATCC 49405 / DSM 1227 / OM5)
(6)
2a
Fer2-1n63D01
D:8-75
2b
Fer2-1n63D02
D:8-75
Family
:
Fer2_2
(24)
Oligotropha carboxidovorans (strain ATCC 49405 / DSM 1227 / OM5)
(6)
3a
Fer2_2-1n63D03
D:76-151
3b
Fer2_2-1n63D04
D:76-151
Clan
:
no clan defined [family: Ald_Xan_dh_C2]
(24)
Family
:
Ald_Xan_dh_C2
(24)
Oligotropha carboxidovorans (strain ATCC 49405 / DSM 1227 / OM5)
(6)
4a
Ald_Xan_dh_C2-1n63E01
E:153-740
4b
Ald_Xan_dh_C2-1n63E02
E:153-740
Clan
:
no clan defined [family: Ald_Xan_dh_C]
(24)
Family
:
Ald_Xan_dh_C
(24)
Oligotropha carboxidovorans (strain ATCC 49405 / DSM 1227 / OM5)
(6)
5a
Ald_Xan_dh_C-1n63E03
E:35-144
5b
Ald_Xan_dh_C-1n63E04
E:35-144
Clan
:
no clan defined [family: CO_deh_flav_C]
(22)
Family
:
CO_deh_flav_C
(22)
Oligotropha carboxidovorans (strain ATCC 49405 / DSM 1227 / OM5)
(6)
6a
CO_deh_flav_C-1n63F03
F:181-282
6b
CO_deh_flav_C-1n63F04
F:181-282
[
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]
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select chains 'A' and 'C'
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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select non-helix/non-sheet protein parts
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show SS bonds with a radius of 100 units (=0.4Å)
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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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