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3I04
Biol. Unit 2
Info
Asym.Unit (925 KB)
Biol.Unit 1 (471 KB)
Biol.Unit 2 (457 KB)
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(1)
Title
:
CYANIDE-BOUND STRUCTURE OF BIFUNCTIONAL CARBON MONOXIDE DEHYDROGENASE/ACETYL-COA SYNTHASE FROM MOORELLA THERMOACETICA, CYANIDE-BOUND C-CLUSTER
Authors
:
Y. Kung, T. I. Doukov, C. L. Drennan
Date
:
24 Jun 09 (Deposition) - 01 Sep 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.15
Chains
:
Asym. Unit : A,B,C,D,M,N,O,P
Biol. Unit 1: A,B,M,N (1x)
Biol. Unit 2: C,D,O,P (1x)
Keywords
:
Protein-Protein Complex, Carbon Dioxide Fixation, Electron Transport, Iron, Iron-Sulfur, Metal-Binding, Nickel, Oxidoreductase, Transport, Transferase, Oxidoreductase-Transferase Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Kung, T. I. Doukov, J. Seravalli, S. W. Ragsdale, C. L. Drennan
Crystallographic Snapshots Of Cyanide- And Water-Bound C-Clusters From Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase.
Biochemistry V. 48 7432 2009
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Hetero Components
(6, 15)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
2a: COPPER (I) ION (CU1a)
2b: COPPER (I) ION (CU1b)
2c: COPPER (I) ION (CU1c)
2d: COPPER (I) ION (CU1d)
3a: CYANIDE ION (CYNa)
3b: CYANIDE ION (CYNb)
3c: CYANIDE ION (CYNc)
3d: CYANIDE ION (CYNd)
4a: GLYCEROL (GOLa)
4b: GLYCEROL (GOLb)
4c: GLYCEROL (GOLc)
4d: GLYCEROL (GOLd)
5a: SODIUM ION (NAa)
5b: SODIUM ION (NAb)
5c: SODIUM ION (NAc)
5d: SODIUM ION (NAd)
6a: NICKEL (II) ION (NIa)
6b: NICKEL (II) ION (NIb)
6c: NICKEL (II) ION (NIc)
6d: NICKEL (II) ION (NId)
7a: IRON/SULFUR CLUSTER (SF4a)
7b: IRON/SULFUR CLUSTER (SF4b)
7c: IRON/SULFUR CLUSTER (SF4c)
7d: IRON/SULFUR CLUSTER (SF4d)
7e: IRON/SULFUR CLUSTER (SF4e)
7f: IRON/SULFUR CLUSTER (SF4f)
7g: IRON/SULFUR CLUSTER (SF4g)
7h: IRON/SULFUR CLUSTER (SF4h)
7i: IRON/SULFUR CLUSTER (SF4i)
7j: IRON/SULFUR CLUSTER (SF4j)
8a: FE(4)-NI(1)-S(4) CLUSTER (XCCa)
8b: FE(4)-NI(1)-S(4) CLUSTER (XCCb)
8c: FE(4)-NI(1)-S(4) CLUSTER (XCCc)
8d: FE(4)-NI(1)-S(4) CLUSTER (XCCd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
2
Ligand/Ion
ACETATE ION
2
CU1
2
Ligand/Ion
COPPER (I) ION
3
CYN
2
Ligand/Ion
CYANIDE ION
4
GOL
2
Ligand/Ion
GLYCEROL
5
NA
-1
Ligand/Ion
SODIUM ION
6
NI
-1
Ligand/Ion
NICKEL (II) ION
7
SF4
5
Ligand/Ion
IRON/SULFUR CLUSTER
8
XCC
2
Ligand/Ion
FE(4)-NI(1)-S(4) CLUSTER
[
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Sites
(19, 19)
Info
All Sites
01: BC1 (SOFTWARE)
02: BC2 (SOFTWARE)
03: BC3 (SOFTWARE)
04: BC4 (SOFTWARE)
05: BC5 (SOFTWARE)
06: BC6 (SOFTWARE)
07: BC7 (SOFTWARE)
08: BC9 (SOFTWARE)
09: CC1 (SOFTWARE)
10: DC1 (SOFTWARE)
11: DC3 (SOFTWARE)
12: DC4 (SOFTWARE)
13: DC5 (SOFTWARE)
14: DC6 (SOFTWARE)
15: DC7 (SOFTWARE)
16: DC8 (SOFTWARE)
17: DC9 (SOFTWARE)
18: EC1 (SOFTWARE)
19: EC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
BC1
SOFTWARE
CYS C:59 , GLY C:62 , CYS C:67 , ARG C:69 , CYS D:59 , GLY D:62 , CYS D:67 , ARG D:69
BINDING SITE FOR RESIDUE SF4 C 700
02
BC2
SOFTWARE
CYS C:68 , CYS C:71 , CYS C:76 , GLY C:88 , CYS C:90 , ARG C:100 , MET C:221
BINDING SITE FOR RESIDUE SF4 C 750
03
BC3
SOFTWARE
HIS C:283 , CYS C:316 , CYS C:317 , PHE C:334 , CYS C:355 , GLY C:469 , CYS C:470 , CYS C:500 , CYS C:550 , SER C:585 , LYS C:587 , CYN C:900 , HOH C:2515
BINDING SITE FOR RESIDUE XCC C 800
04
BC4
SOFTWARE
CYS D:68 , CYS D:71 , ALA D:73 , CYS D:76 , GLY D:88 , CYS D:90 , ARG D:100
BINDING SITE FOR RESIDUE SF4 D 750
05
BC5
SOFTWARE
HIS C:113 , CYS C:550 , LYS C:587 , ILE C:591 , XCC C:800 , HOH C:2515
BINDING SITE FOR RESIDUE CYN C 900
06
BC6
SOFTWARE
THR C:81 , ALA C:94 , TRP C:95 , SER C:613 , ASP C:614 , LEU C:615 , HIS O:27
BINDING SITE FOR RESIDUE GOL C 963
07
BC7
SOFTWARE
HIS D:283 , CYS D:316 , CYS D:317 , PHE D:334 , CYS D:355 , GLY D:469 , CYS D:470 , CYS D:500 , CYS D:550 , SER D:585 , LYS D:587 , CYN D:900 , HOH D:2516
BINDING SITE FOR RESIDUE XCC D 800
08
BC9
SOFTWARE
HIS D:113 , CYS D:550 , LYS D:587 , ILE D:591 , XCC D:800 , HOH D:2516
BINDING SITE FOR RESIDUE CYN D 900
09
CC1
SOFTWARE
ALA D:94 , TRP D:95 , SER D:613 , ASP D:614 , LEU D:615 , HOH D:1617 , HIS P:27
BINDING SITE FOR RESIDUE GOL D 963
10
DC1
SOFTWARE
CYS O:509 , CYS O:595 , CYS O:597 , SF4 O:900 , NI O:951 , ACT O:953
BINDING SITE FOR RESIDUE CU1 O 950
11
DC3
SOFTWARE
ILE O:146 , CYS O:506 , LEU O:508 , CYS O:509 , CYS O:518 , GLY O:526 , LEU O:527 , CYS O:528 , CYS O:597 , CU1 O:950
BINDING SITE FOR RESIDUE SF4 O 900
12
DC4
SOFTWARE
PHE O:328 , GLU O:331 , ASN O:412 , GLY O:414 , LEU O:417 , HOH O:731
BINDING SITE FOR RESIDUE NA O 730
13
DC5
SOFTWARE
LEU O:527 , CYS O:595 , GLY O:596 , CYS O:597 , PHE O:598 , CU1 O:950 , ACT O:953
BINDING SITE FOR RESIDUE NI O 951
14
DC6
SOFTWARE
CYS P:509 , CYS P:595 , CYS P:597 , SF4 P:900 , NI P:951 , ACT P:953
BINDING SITE FOR RESIDUE CU1 P 950
15
DC7
SOFTWARE
GLY O:145 , PHE O:229 , CYS O:509 , CYS O:595 , CYS O:597 , CU1 O:950 , NI O:951
BINDING SITE FOR RESIDUE ACT O 953
16
DC8
SOFTWARE
ILE P:146 , CYS P:506 , CYS P:509 , CYS P:518 , GLY P:526 , LEU P:527 , CYS P:528 , VAL P:531 , CYS P:597 , CU1 P:950
BINDING SITE FOR RESIDUE SF4 P 900
17
DC9
SOFTWARE
PHE P:328 , GLU P:331 , ASN P:412 , GLY P:414 , LEU P:417 , HOH P:731
BINDING SITE FOR RESIDUE NA P 730
18
EC1
SOFTWARE
CYS P:595 , GLY P:596 , CYS P:597 , CU1 P:950 , ACT P:953
BINDING SITE FOR RESIDUE NI P 951
19
EC2
SOFTWARE
GLY P:145 , ILE P:146 , VAL P:149 , PHE P:229 , CYS P:509 , CYS P:597 , CU1 P:950 , NI P:951
BINDING SITE FOR RESIDUE ACT P 953
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
Sorry, no Info available
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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
(2, 8)
Info
All SCOP Domains
1a: SCOP_d3i04m_ (M:)
1b: SCOP_d3i04n_ (N:)
1c: SCOP_d3i04o_ (O:)
1d: SCOP_d3i04p_ (P:)
2a: SCOP_d3i04a_ (A:)
2b: SCOP_d3i04b_ (B:)
2c: SCOP_d3i04c_ (C:)
2d: SCOP_d3i04d_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
Prismane protein-like
(31)
Superfamily
:
Prismane protein-like
(31)
Family
:
Acetyl-CoA synthase
(6)
Protein domain
:
automated matches
(3)
Moorella thermoacetica [TaxId: 1525]
(3)
1a
d3i04m_
M:
1b
d3i04n_
N:
1c
d3i04o_
O:
1d
d3i04p_
P:
Family
:
Carbon monoxide dehydrogenase
(15)
Protein domain
:
automated matches
(3)
Moorella thermoacetica [TaxId: 1525]
(3)
2a
d3i04a_
A:
2b
d3i04b_
B:
2c
d3i04c_
C:
2d
d3i04d_
D:
[
close SCOP info
]
CATH Domains
(6, 32)
Info
all CATH domains
1a: CATH_3i04M03 (M:318-493)
1b: CATH_3i04N03 (N:318-493)
1c: CATH_3i04O03 (O:318-493)
1d: CATH_3i04P03 (P:318-493)
2a: CATH_3i04M05 (M:600-728)
2b: CATH_3i04N05 (N:600-728)
2c: CATH_3i04O05 (O:600-728)
2d: CATH_3i04P05 (P:600-728)
3a: CATH_3i04M04 (M:494-584)
3b: CATH_3i04N04 (N:494-584)
3c: CATH_3i04O04 (O:494-584)
3d: CATH_3i04P04 (P:494-584)
4a: CATH_3i04A02 (A:260-430)
4b: CATH_3i04A03 (A:433-660)
4c: CATH_3i04B03 (B:433-660)
4d: CATH_3i04C03 (C:433-660)
4e: CATH_3i04D03 (D:433-660)
4f: CATH_3i04M02 (M:122-311)
4g: CATH_3i04N02 (N:122-311)
4h: CATH_3i04O02 (O:122-311)
4i: CATH_3i04P02 (P:122-311)
4j: CATH_3i04B02 (B:260-430)
4k: CATH_3i04C02 (C:260-430)
4l: CATH_3i04D02 (D:260-430)
5a: CATH_3i04M01 (M:2-121)
5b: CATH_3i04N01 (N:2-121)
5c: CATH_3i04O01 (O:2-121)
5d: CATH_3i04P01 (P:2-121)
6a: CATH_3i04A01 (A:83-259)
6b: CATH_3i04B01 (B:83-259)
6c: CATH_3i04C01 (C:83-259)
6d: CATH_3i04D01 (D:83-259)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3
(6)
Homologous Superfamily
:
Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3
(6)
Clostridium thermoaceticum (Moorella thermoacetica)
(2)
1a
3i04M03
M:318-493
1b
3i04N03
N:318-493
1c
3i04O03
O:318-493
1d
3i04P03
P:318-493
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5
(6)
Homologous Superfamily
:
Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5
(6)
Clostridium thermoaceticum (Moorella thermoacetica)
(2)
2a
3i04M05
M:600-728
2b
3i04N05
N:600-728
2c
3i04O05
O:600-728
2d
3i04P05
P:600-728
Topology
:
Ribonuclease HI; Chain A
(10)
Homologous Superfamily
:
Carbon monoxide dehydrogenase alpha subunit. Chain D, domain 4
(6)
Clostridium thermoaceticum (Moorella thermoacetica)
(2)
3a
3i04M04
M:494-584
3b
3i04N04
N:494-584
3c
3i04O04
O:494-584
3d
3i04P04
P:494-584
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.2030, no name defined]
(25)
Clostridium thermoaceticum (Moorella thermoacetica)
(2)
4a
3i04A02
A:260-430
4b
3i04A03
A:433-660
4c
3i04B03
B:433-660
4d
3i04C03
C:433-660
4e
3i04D03
D:433-660
4f
3i04M02
M:122-311
4g
3i04N02
N:122-311
4h
3i04O02
O:122-311
4i
3i04P02
P:122-311
4j
3i04B02
B:260-430
4k
3i04C02
C:260-430
4l
3i04D02
D:260-430
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Helicase, Ruva Protein; domain 3
(218)
Homologous Superfamily
:
Carbon monoxide dehydrogenase alpha subunit. Chain M, domain 1
(6)
Clostridium thermoaceticum (Moorella thermoacetica)
(2)
5a
3i04M01
M:2-121
5b
3i04N01
N:2-121
5c
3i04O01
O:2-121
5d
3i04P01
P:2-121
Architecture
:
Up-down Bundle
(3216)
Topology
:
Substrate Binding Domain Of Dnak; Chain:A; Domain 2
(103)
Homologous Superfamily
:
[code=1.20.1270.30, no name defined]
(14)
Clostridium thermoaceticum (Moorella thermoacetica)
(2)
6a
3i04A01
A:83-259
6b
3i04B01
B:83-259
6c
3i04C01
C:83-259
6d
3i04D01
D:83-259
[
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Pfam Domains
(0, 0)
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all PFAM domains
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