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1E08
Theor. Model
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Theoretical Model (97 KB)
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(1)
Title
:
STRUCTURAL MODEL OF THE [FE]-HYDROGENASE/CYTOCHROME C553 COMPLEX COMBINING NMR AND SOFT-DOCKING
Authors
:
X. Morelli, M. Czjzek, C. E. Hatchikian, O. Bornet, J. C. Fontecilla-Camps, N. P. Palma, J. J. G. Moura, F. Guerlesquin
Date
:
13 Mar 00 (Deposition) - 25 Aug 00 (Release) - 24 Feb 09 (Revision)
Method
:
SOLUTION NMR; THEORETICAL MODEL
Resolution
:
NOT APPLICABLE
Chains
:
Theor. Model : A,D,E
Keywords
:
Hydrogenase, Cytochrome C553, Electron Transfer Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
X. Morelli, M. Czjzek, C. E. Hatchikian, O. Bornet, J. C. Fontecilla-Camps, N. P. Palma, J. J. Moura, F. Guerlesquin
Structural Model Of The Fe-Hydrogenase/Cytochrome C553 Complex Combining Transverse Relaxation- Optimized Spectroscopy Experiments And Soft Docking Calculations.
J. Biol. Chem. V. 275 23204 2000
(for further references see the
PDB file header
)
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Hetero Components
(7, 12)
Info
All Hetero Components
1a: CARBON MONOXIDE (CMOa)
1b: CARBON MONOXIDE (CMOb)
2a: CYANIDE ION (CYNa)
2b: CYANIDE ION (CYNb)
3a: FE (II) ION (FE2a)
3b: FE (II) ION (FE2b)
4a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
5a: 1,3-PROPANEDITHIOL (PDTa)
6a: IRON/SULFUR CLUSTER (SF4a)
6b: IRON/SULFUR CLUSTER (SF4b)
6c: IRON/SULFUR CLUSTER (SF4c)
7a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CMO
2
Ligand/Ion
CARBON MONOXIDE
2
CYN
2
Ligand/Ion
CYANIDE ION
3
FE2
2
Ligand/Ion
FE (II) ION
4
HEM
1
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
5
PDT
1
Ligand/Ion
1,3-PROPANEDITHIOL
6
SF4
3
Ligand/Ion
IRON/SULFUR CLUSTER
7
ZN
1
Ligand/Ion
ZINC ION
[
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Sites
(12, 12)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PDT A:4 , FE2 A:6 , CYN A:7 , CYN A:8 , CMO A:9 , CMO A:10 , HOH A:11 , ALA A:293
BINDING SITE FOR RESIDUE FE2 A 5
02
AC2
SOFTWARE
PDT A:4 , FE2 A:5 , CYN A:7 , CYN A:8 , CMO A:9 , CMO A:10 , HOH A:11 , PRO A:108 , THR A:145 , ALA A:149
BINDING SITE FOR RESIDUE FE2 A 6
03
AC3
SOFTWARE
HIS D:82 , LYS D:83 , HIS D:85 , ASP D:86
BINDING SITE FOR RESIDUE ZN D 12
04
AC4
SOFTWARE
PDT A:4 , FE2 A:5 , FE2 A:6 , CYN A:8 , CMO A:9 , CMO A:10 , HOH A:11 , ALA A:149 , PRO A:203 , PHE A:296
BINDING SITE FOR RESIDUE CYN A 7
05
AC5
SOFTWARE
PDT A:4 , FE2 A:5 , FE2 A:6 , CYN A:7 , CMO A:9 , CMO A:10 , HOH A:11 , PRO A:108 , ALA A:109 , ALA A:293 , THR A:294 , ILE A:295 , PHE A:296
BINDING SITE FOR RESIDUE CYN A 8
06
AC6
SOFTWARE
ILE A:30 , LYS A:34 , CYS A:35 , ILE A:36 , GLY A:37 , CYS A:38 , ASP A:39 , CYS A:41 , SER A:42 , HIS A:58 , HIS A:75 , CYS A:76 , ILE A:81
BINDING SITE FOR RESIDUE SF4 A 1
07
AC7
SOFTWARE
VAL A:28 , TYR A:44 , CYS A:45 , CYS A:66 , ASN A:68 , CYS A:69 , GLY A:70 , CYS A:72
BINDING SITE FOR RESIDUE SF4 A 2
08
AC8
SOFTWARE
CYS A:69 , CYS A:179 , PRO A:180 , CYS A:234 , LYS A:237 , MET A:376 , ALA A:377 , CYS A:378 , CYS A:382 , GLY A:385
BINDING SITE FOR RESIDUE SF4 A 3
09
AC9
SOFTWARE
FE2 A:5 , FE2 A:6 , CYN A:7 , CYN A:8 , CMO A:9 , CMO A:10 , ALA A:107 , PRO A:108 , ALA A:109 , VAL A:110 , LYS A:237 , ILE A:295 , PHE A:296 , GLY A:297
BINDING SITE FOR RESIDUE PDT A 4
10
BC1
SOFTWARE
PDT A:4 , FE2 A:5 , FE2 A:6 , CYN A:7 , CYN A:8 , CMO A:10 , HOH A:11 , ALA A:107 , PRO A:108 , THR A:145 , PRO A:203
BINDING SITE FOR RESIDUE CMO A 9
11
BC2
SOFTWARE
PDT A:4 , FE2 A:5 , FE2 A:6 , CYN A:7 , CYN A:8 , CMO A:9 , HOH A:11 , ALA A:293 , THR A:294 , ILE A:295 , PHE A:296
BINDING SITE FOR RESIDUE CMO A 10
12
BC3
SOFTWARE
CYS A:38 , GLY A:55 , CYS E:10 , CYS E:13 , HIS E:14 , MET E:23 , GLY E:24 , ALA E:26 , LYS E:27 , GLN E:32 , LEU E:37 , MET E:41 , TYR E:44 , TYR E:49 , GLY E:51 , GLU E:52 , ARG E:53 , MET E:56 , MET E:57 , TYR E:64
BINDING SITE FOR RESIDUE HEM E 80
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 3)
Info
All PROSITE Patterns/Profiles
1: 4FE4S_FER_2 (-|A:59-86)
2: 4FE4S_FER_1 (A:35-46|A:66-77)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
4FE4S_FER_2
PS51379
4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
PHFL_DESVH
26-57
59-86
1
-
A:59-86
2
4FE4S_FER_1
PS00198
4Fe-4S ferredoxin-type iron-sulfur binding region signature.
PHFL_DESVH
35-46
66-77
2
A:35-46
A:66-77
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Exons
(0, 0)
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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
(1, 3)
Info
All SCOP Domains
1a: SCOP_d1e08a_ (A:)
1b: SCOP_d1e08d_ (D:)
1c: SCOP_d1e08e_ (E:)
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Protein Domains
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Class
:
Low resolution protein structures
(283)
Fold
:
Electron transport chains
(4)
Superfamily
:
Electron transport chains
(4)
Family
:
Electron transport chains
(4)
Protein domain
:
[Fe]-hydrogenase/cytochrome c553 complex
(1)
interspecies complex: Desulfovibrio desulfuricans and Desulfovibrio vulgaris
(1)
1a
d1e08a_
A:
1b
d1e08d_
D:
1c
d1e08e_
E:
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CATH Domains
(0, 0)
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Sorry, no Info available
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Pfam Domains
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Chain A
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Chain E
Asymmetric Unit 1
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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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