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2Z8Y
Asym. Unit
Info
Asym.Unit (906 KB)
Biol.Unit 1 (459 KB)
Biol.Unit 2 (449 KB)
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(1)
Title
:
XENON-BOUND STRUCTURE OF BIFUNCTIONAL CARBON MONOXIDE DEHYDROGENASE/ACETYL-COA SYNTHASE(CODH/ACS) FROM MOORELLA THERMOACETICA
Authors
:
T. I. Doukov, L. C. Blasiak, C. L. Drennan
Date
:
12 Sep 07 (Deposition) - 11 Mar 08 (Release) - 12 Nov 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.51
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
:
Xenon, Carbon Monoxide (Co) Channel, Nickel-Iron-Sulfur (Ni-Fe-S) Cluster, Nickel-Copper-Iron-Sulfur (Ni-Cu-Fe-S) Cluster, Helical Domain, Rossmann Fold, Clostridium Thermoaceticum, Wood-Ljundahl Pathway, Carbon Dioxide Fixation, Electron Transport, Metal-Binding, Oxidoreductase, Transport, Transferase, Oxidoreductase-Transferase Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. I. Doukov, L. C. Blasiak, J. Seravalli, S. W. Ragsdale, C. L. Drennan
Xenon In And At The End Of The Tunnel Of Bifunctional Carbo Monoxide Dehydrogenase/Acetyl-Coa Synthase
Biochemistry V. 47 3474 2008
[
close entry info
]
Hetero Components
(6, 71)
Info
All Hetero Components
1a: COPPER (I) ION (CU1a)
1b: COPPER (I) ION (CU1b)
1c: COPPER (I) ION (CU1c)
1d: COPPER (I) ION (CU1d)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
2i: GLYCEROL (GOLi)
2j: GLYCEROL (GOLj)
2k: GLYCEROL (GOLk)
3a: NICKEL (II) ION (NIa)
3b: NICKEL (II) ION (NIb)
3c: NICKEL (II) ION (NIc)
3d: NICKEL (II) ION (NId)
4a: IRON/SULFUR CLUSTER (SF4a)
4b: IRON/SULFUR CLUSTER (SF4b)
4c: IRON/SULFUR CLUSTER (SF4c)
4d: IRON/SULFUR CLUSTER (SF4d)
4e: IRON/SULFUR CLUSTER (SF4e)
4f: IRON/SULFUR CLUSTER (SF4f)
4g: IRON/SULFUR CLUSTER (SF4g)
4h: IRON/SULFUR CLUSTER (SF4h)
4i: IRON/SULFUR CLUSTER (SF4i)
4j: IRON/SULFUR CLUSTER (SF4j)
5a: FE(4)-NI(1)-S(4) CLUSTER (XCCa)
5b: FE(4)-NI(1)-S(4) CLUSTER (XCCb)
5c: FE(4)-NI(1)-S(4) CLUSTER (XCCc)
5d: FE(4)-NI(1)-S(4) CLUSTER (XCCd)
6a: XENON (XEa)
6aa: XENON (XEaa)
6ab: XENON (XEab)
6ac: XENON (XEac)
6ad: XENON (XEad)
6ae: XENON (XEae)
6af: XENON (XEaf)
6ag: XENON (XEag)
6ah: XENON (XEah)
6ai: XENON (XEai)
6aj: XENON (XEaj)
6ak: XENON (XEak)
6al: XENON (XEal)
6b: XENON (XEb)
6c: XENON (XEc)
6d: XENON (XEd)
6e: XENON (XEe)
6f: XENON (XEf)
6g: XENON (XEg)
6h: XENON (XEh)
6i: XENON (XEi)
6j: XENON (XEj)
6k: XENON (XEk)
6l: XENON (XEl)
6m: XENON (XEm)
6n: XENON (XEn)
6o: XENON (XEo)
6p: XENON (XEp)
6q: XENON (XEq)
6r: XENON (XEr)
6s: XENON (XEs)
6t: XENON (XEt)
6u: XENON (XEu)
6v: XENON (XEv)
6w: XENON (XEw)
6x: XENON (XEx)
6y: XENON (XEy)
6z: XENON (XEz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CU1
4
Ligand/Ion
COPPER (I) ION
2
GOL
11
Ligand/Ion
GLYCEROL
3
NI
4
Ligand/Ion
NICKEL (II) ION
4
SF4
10
Ligand/Ion
IRON/SULFUR CLUSTER
5
XCC
4
Ligand/Ion
FE(4)-NI(1)-S(4) CLUSTER
6
XE
38
Ligand/Ion
XENON
[
close Hetero Component info
]
Sites
(50, 50)
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)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
45: EC9 (SOFTWARE)
46: FC1 (SOFTWARE)
47: FC2 (SOFTWARE)
48: FC3 (SOFTWARE)
49: FC4 (SOFTWARE)
50: FC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS M:509 , CYS M:595 , CYS M:597
BINDING SITE FOR RESIDUE CU1 M 950
02
AC2
SOFTWARE
CYS M:595 , GLY M:596 , CYS M:597 , PHE M:598
BINDING SITE FOR RESIDUE NI M 951
03
AC3
SOFTWARE
CYS N:509 , CYS N:595 , CYS N:597
BINDING SITE FOR RESIDUE CU1 N 950
04
AC4
SOFTWARE
CYS N:595 , GLY N:596 , CYS N:597 , PHE N:598
BINDING SITE FOR RESIDUE NI N 951
05
AC5
SOFTWARE
CYS O:509 , CYS O:595 , CYS O:597
BINDING SITE FOR RESIDUE CU1 O 950
06
AC6
SOFTWARE
LEU O:527 , CYS O:595 , GLY O:596 , CYS O:597 , PHE O:598
BINDING SITE FOR RESIDUE NI O 951
07
AC7
SOFTWARE
CYS P:509 , CYS P:595 , CYS P:597
BINDING SITE FOR RESIDUE CU1 P 950
08
AC8
SOFTWARE
CYS P:595 , GLY P:596 , CYS P:597
BINDING SITE FOR RESIDUE NI P 951
09
AC9
SOFTWARE
CYS A:68 , CYS A:71 , ALA A:73 , GLY A:74 , CYS A:76 , GLY A:88 , CYS A:90 , MET A:221
BINDING SITE FOR RESIDUE SF4 A 700
10
BC1
SOFTWARE
CYS A:59 , GLY A:62 , CYS A:67 , ARG A:69 , CYS B:59 , GLY B:62 , CYS B:67 , ARG B:69
BINDING SITE FOR RESIDUE SF4 A 750
11
BC2
SOFTWARE
HIS A:283 , CYS A:316 , CYS A:317 , CYS A:355 , GLY A:469 , CYS A:470 , CYS A:500 , CYS A:550 , SER A:585 , LYS A:587
BINDING SITE FOR RESIDUE XCC A 800
12
BC3
SOFTWARE
CYS B:68 , CYS B:71 , ALA B:73 , GLY B:74 , CYS B:76 , GLY B:88 , CYS B:90 , ARG B:100 , MET B:221
BINDING SITE FOR RESIDUE SF4 B 700
13
BC4
SOFTWARE
HIS B:283 , CYS B:316 , CYS B:317 , CYS B:355 , GLY B:469 , CYS B:470 , CYS B:500 , CYS B:550 , SER B:585 , LYS B:587
BINDING SITE FOR RESIDUE XCC B 800
14
BC5
SOFTWARE
CYS C:68 , CYS C:71 , GLY C:74 , CYS C:76 , CYS C:90 , ARG C:100 , MET C:221
BINDING SITE FOR RESIDUE SF4 C 700
15
BC6
SOFTWARE
CYS C:59 , GLY C:62 , CYS C:67 , ARG C:69 , CYS D:59 , ILE D:61 , GLY D:62 , CYS D:67 , ARG D:69
BINDING SITE FOR RESIDUE SF4 C 750
16
BC7
SOFTWARE
HIS C:283 , CYS C:316 , CYS C:317 , CYS C:355 , GLY C:469 , CYS C:470 , CYS C:500 , CYS C:550 , SER C:585 , LYS C:587
BINDING SITE FOR RESIDUE XCC C 800
17
BC8
SOFTWARE
CYS D:68 , CYS D:71 , ALA D:73 , GLY D:74 , CYS D:76 , CYS D:90 , ARG D:100
BINDING SITE FOR RESIDUE SF4 D 700
18
BC9
SOFTWARE
HIS D:283 , CYS D:316 , CYS D:317 , CYS D:355 , GLY D:469 , CYS D:470 , CYS D:500 , CYS D:550 , SER D:585 , LYS D:587
BINDING SITE FOR RESIDUE XCC D 800
19
CC1
SOFTWARE
ILE M:146 , CYS M:506 , CYS M:509 , CYS M:518 , GLY M:526 , LEU M:527 , CYS M:528 , CYS M:597
BINDING SITE FOR RESIDUE SF4 M 900
20
CC2
SOFTWARE
ILE N:146 , CYS N:506 , LEU N:508 , CYS N:509 , CYS N:518 , CYS N:528 , CYS N:597
BINDING SITE FOR RESIDUE SF4 N 900
21
CC3
SOFTWARE
CYS O:506 , LEU O:508 , CYS O:509 , CYS O:518 , GLY O:526 , LEU O:527 , CYS O:528 , CYS O:595 , CYS O:597
BINDING SITE FOR RESIDUE SF4 O 900
22
CC4
SOFTWARE
CYS P:506 , LEU P:508 , CYS P:509 , CYS P:518 , LEU P:527 , CYS P:528 , CYS P:597
BINDING SITE FOR RESIDUE SF4 P 900
23
CC5
SOFTWARE
CYS B:468 , ALA B:580 , THR B:602
BINDING SITE FOR RESIDUE XE B 1001
24
CC6
SOFTWARE
ILE B:106
BINDING SITE FOR RESIDUE XE B 1003
25
CC7
SOFTWARE
GLU N:156 , TYR N:221
BINDING SITE FOR RESIDUE XE N 1008
26
CC8
SOFTWARE
TYR B:388 , SER B:396 , ALA B:400
BINDING SITE FOR RESIDUE XE B 1010
27
CC9
SOFTWARE
CYS A:468 , GLY A:592 , THR A:602
BINDING SITE FOR RESIDUE XE A 1001
28
DC1
SOFTWARE
ILE A:106 , ALA A:234 , LEU A:620
BINDING SITE FOR RESIDUE XE A 1003
29
DC2
SOFTWARE
PHE M:229
BINDING SITE FOR RESIDUE XE M 1008
30
DC3
SOFTWARE
LEU A:287 , SER A:396
BINDING SITE FOR RESIDUE XE A 1010
31
DC4
SOFTWARE
CYS D:468 , THR D:602
BINDING SITE FOR RESIDUE XE D 1001
32
DC5
SOFTWARE
LEU D:620
BINDING SITE FOR RESIDUE XE D 1003
33
DC6
SOFTWARE
PHE P:229
BINDING SITE FOR RESIDUE XE P 1009
34
DC7
SOFTWARE
TYR D:388 , SER D:396 , ALA D:400
BINDING SITE FOR RESIDUE XE D 1010
35
DC8
SOFTWARE
CYS C:468 , ALA C:580 , THR C:602
BINDING SITE FOR RESIDUE XE C 1001
36
DC9
SOFTWARE
LEU C:620
BINDING SITE FOR RESIDUE XE C 1003
37
EC1
SOFTWARE
ILE O:215
BINDING SITE FOR RESIDUE XE O 1006
38
EC2
SOFTWARE
PHE O:229
BINDING SITE FOR RESIDUE XE O 1009
39
EC3
SOFTWARE
TYR C:388 , SER C:396
BINDING SITE FOR RESIDUE XE C 1010
40
EC4
SOFTWARE
ILE A:46 , ALA A:362 , HOH A:1027 , HOH A:1113
BINDING SITE FOR RESIDUE GOL A 860
41
EC5
SOFTWARE
SER A:14 , GLU A:15 , ALA A:16 , ARG A:18
BINDING SITE FOR RESIDUE GOL A 861
42
EC6
SOFTWARE
PRO A:2 , ARG A:3 , GLN A:622 , SER A:625 , HOH A:1112 , GLU M:257 , HIS M:258 , ASP M:259 , HOH M:1161
BINDING SITE FOR RESIDUE GOL A 862
43
EC7
SOFTWARE
SER A:613 , ASP A:614 , HIS M:27
BINDING SITE FOR RESIDUE GOL A 863
44
EC8
SOFTWARE
HOH A:1160 , ILE B:46 , ALA B:362 , HOH B:1027 , HOH B:1145
BINDING SITE FOR RESIDUE GOL B 860
45
EC9
SOFTWARE
PRO B:13 , SER B:14 , GLU B:15 , ALA B:16 , ARG B:18 , HOH B:1143
BINDING SITE FOR RESIDUE GOL B 861
46
FC1
SOFTWARE
SER B:613 , ASP B:614 , LEU B:615 , HOH B:1158 , HIS N:27
BINDING SITE FOR RESIDUE GOL B 863
47
FC2
SOFTWARE
ILE C:46 , HOH C:1137
BINDING SITE FOR RESIDUE GOL C 860
48
FC3
SOFTWARE
SER C:8 , HIS C:9 , ASN C:10 , ARG C:12 , PRO C:13 , SER C:14 , ARG C:643 , LYS C:644
BINDING SITE FOR RESIDUE GOL C 861
49
FC4
SOFTWARE
ILE D:46
BINDING SITE FOR RESIDUE GOL D 860
50
FC5
SOFTWARE
ALA D:94 , TRP D:95 , GLY D:612 , SER D:613 , ASP D:614 , LEU D:615 , HOH D:1069 , HIS P:27
BINDING SITE FOR RESIDUE GOL D 863
[
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_d2z8ym_ (M:)
1b: SCOP_d2z8yo_ (O:)
1c: SCOP_d2z8yp_ (P:)
1d: SCOP_d2z8yn_ (N:)
2a: SCOP_d2z8ya_ (A:)
2b: SCOP_d2z8yc_ (C:)
2c: SCOP_d2z8yd_ (D:)
2d: SCOP_d2z8yb_ (B:)
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
d2z8ym_
M:
1b
d2z8yo_
O:
1c
d2z8yp_
P:
1d
d2z8yn_
N:
Family
:
Carbon monoxide dehydrogenase
(15)
Protein domain
:
automated matches
(3)
Moorella thermoacetica [TaxId: 1525]
(3)
2a
d2z8ya_
A:
2b
d2z8yc_
C:
2c
d2z8yd_
D:
2d
d2z8yb_
B:
[
close SCOP info
]
CATH Domains
(6, 32)
Info
all CATH domains
1a: CATH_2z8yM03 (M:318-493)
1b: CATH_2z8yN03 (N:318-493)
1c: CATH_2z8yO03 (O:318-493)
1d: CATH_2z8yP03 (P:318-493)
2a: CATH_2z8yM05 (M:600-728)
2b: CATH_2z8yN05 (N:600-728)
2c: CATH_2z8yP05 (P:600-728)
2d: CATH_2z8yO05 (O:600-728)
3a: CATH_2z8yM04 (M:494-584)
3b: CATH_2z8yN04 (N:494-584)
3c: CATH_2z8yO04 (O:494-584)
3d: CATH_2z8yP04 (P:494-584)
4a: CATH_2z8yA02 (A:260-430)
4b: CATH_2z8yA03 (A:433-660)
4c: CATH_2z8yB03 (B:433-660)
4d: CATH_2z8yC03 (C:433-660)
4e: CATH_2z8yD03 (D:433-660)
4f: CATH_2z8yM02 (M:122-311)
4g: CATH_2z8yN02 (N:122-311)
4h: CATH_2z8yO02 (O:122-311)
4i: CATH_2z8yP02 (P:122-311)
4j: CATH_2z8yB02 (B:260-430)
4k: CATH_2z8yC02 (C:260-430)
4l: CATH_2z8yD02 (D:260-430)
5a: CATH_2z8yM01 (M:2-121)
5b: CATH_2z8yN01 (N:2-121)
5c: CATH_2z8yO01 (O:2-121)
5d: CATH_2z8yP01 (P:2-121)
6a: CATH_2z8yA01 (A:83-259)
6b: CATH_2z8yB01 (B:83-259)
6c: CATH_2z8yC01 (C:83-259)
6d: CATH_2z8yD01 (D:83-259)
View:
Select:
Label:
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)
Moorella thermoacetica. Organism_taxid: 1525.
(3)
1a
2z8yM03
M:318-493
1b
2z8yN03
N:318-493
1c
2z8yO03
O:318-493
1d
2z8yP03
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)
Moorella thermoacetica. Organism_taxid: 1525.
(3)
2a
2z8yM05
M:600-728
2b
2z8yN05
N:600-728
2c
2z8yP05
P:600-728
2d
2z8yO05
O:600-728
Topology
:
Ribonuclease HI; Chain A
(10)
Homologous Superfamily
:
Carbon monoxide dehydrogenase alpha subunit. Chain D, domain 4
(6)
Moorella thermoacetica. Organism_taxid: 1525.
(3)
3a
2z8yM04
M:494-584
3b
2z8yN04
N:494-584
3c
2z8yO04
O:494-584
3d
2z8yP04
P:494-584
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.2030, no name defined]
(25)
Moorella thermoacetica. Organism_taxid: 1525.
(3)
4a
2z8yA02
A:260-430
4b
2z8yA03
A:433-660
4c
2z8yB03
B:433-660
4d
2z8yC03
C:433-660
4e
2z8yD03
D:433-660
4f
2z8yM02
M:122-311
4g
2z8yN02
N:122-311
4h
2z8yO02
O:122-311
4i
2z8yP02
P:122-311
4j
2z8yB02
B:260-430
4k
2z8yC02
C:260-430
4l
2z8yD02
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)
Moorella thermoacetica. Organism_taxid: 1525.
(3)
5a
2z8yM01
M:2-121
5b
2z8yN01
N:2-121
5c
2z8yO01
O:2-121
5d
2z8yP01
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)
Moorella thermoacetica. Organism_taxid: 1525.
(3)
6a
2z8yA01
A:83-259
6b
2z8yB01
B:83-259
6c
2z8yC01
C:83-259
6d
2z8yD01
D:83-259
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Pfam Domains
(2, 8)
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all PFAM domains
1a: PFAM_CdhC_2z8yP01 (P:317-729)
1b: PFAM_CdhC_2z8yP02 (P:317-729)
1c: PFAM_CdhC_2z8yP03 (P:317-729)
1d: PFAM_CdhC_2z8yP04 (P:317-729)
2a: PFAM_Prismane_2z8yD01 (D:66-642)
2b: PFAM_Prismane_2z8yD02 (D:66-642)
2c: PFAM_Prismane_2z8yD03 (D:66-642)
2d: PFAM_Prismane_2z8yD04 (D:66-642)
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Clan
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no clan defined [family: CdhC]
(4)
Family
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CdhC
(4)
Moorella thermoacetica (Clostridium thermoaceticum)
(3)
1a
CdhC-2z8yP01
P:317-729
1b
CdhC-2z8yP02
P:317-729
1c
CdhC-2z8yP03
P:317-729
1d
CdhC-2z8yP04
P:317-729
Clan
:
no clan defined [family: Prismane]
(9)
Family
:
Prismane
(9)
Moorella thermoacetica (Clostridium thermoaceticum)
(3)
2a
Prismane-2z8yD01
D:66-642
2b
Prismane-2z8yD02
D:66-642
2c
Prismane-2z8yD03
D:66-642
2d
Prismane-2z8yD04
D:66-642
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