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4GD3
Biol. Unit 2
Info
Asym.Unit (1.3 MB)
Biol.Unit 1 (674 KB)
Biol.Unit 2 (312 KB)
Biol.Unit 3 (374 KB)
Biol.Unit 4 (674 KB)
Biol.Unit 5 (311 KB)
Biol.Unit 6 (375 KB)
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(1)
Title
:
STRUCTURE OF E. COLI HYDROGENASE-1 IN COMPLEX WITH CYTOCHROME B
Authors
:
A. Volbeda, J. C. Fontecilla-Camps, C. Darnault
Date
:
31 Jul 12 (Deposition) - 02 Jan 13 (Release) - 30 Jan 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.30
Chains
:
Asym. Unit : A,B,J,K,L,M,Q,R,S,T
Biol. Unit 1: A,L,M,S,T (1x)
Biol. Unit 2: L,S (1x)
Biol. Unit 3: A,M,T (1x)
Biol. Unit 4: B,J,K,Q,R (1x)
Biol. Unit 5: J,Q (1x)
Biol. Unit 6: B,K,R (1x)
Keywords
:
O2-Tolerant H2:Quinone Oxidoreductase, Membrane-Bound, Ni-Fe- Hydrogenase-Cytochrome B Complex, Oxidoreductase-Electron Transport Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Volbeda, C. Darnault, A. Parkin, F. Sargent, F. A. Armstrong, J. C. Fontecilla-Camps
Crystal Structure Of The O(2)-Tolerant Membrane-Bound Hydrogenase 1 From Escherichia Coli In Complex With Its Cognate Cytochrome B.
Structure V. 21 184 2013
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 4)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
1e: CHLORIDE ION (CLe)
1f: CHLORIDE ION (CLf)
1g: CHLORIDE ION (CLg)
1h: CHLORIDE ION (CLh)
1i: CHLORIDE ION (CLi)
1j: CHLORIDE ION (CLj)
2a: FE4-S3 CLUSTER (F4Sa)
2b: FE4-S3 CLUSTER (F4Sb)
2c: FE4-S3 CLUSTER (F4Sc)
2d: FE4-S3 CLUSTER (F4Sd)
3a: CARBONMONOXIDE-(DICYANO) IRON (FCOa)
3b: CARBONMONOXIDE-(DICYANO) IRON (FCOb)
3c: CARBONMONOXIDE-(DICYANO) IRON (FCOc)
3d: CARBONMONOXIDE-(DICYANO) IRON (FCOd)
4a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
4b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
5a: DODECYL-BETA-D-MALTOSIDE (LMTa)
5b: DODECYL-BETA-D-MALTOSIDE (LMTb)
5c: DODECYL-BETA-D-MALTOSIDE (LMTc)
5d: DODECYL-BETA-D-MALTOSIDE (LMTd)
6a: MAGNESIUM ION (MGa)
6b: MAGNESIUM ION (MGb)
6c: MAGNESIUM ION (MGc)
6d: MAGNESIUM ION (MGd)
7a: NICKEL (II) ION (NIa)
7b: NICKEL (II) ION (NIb)
7c: NICKEL (II) ION (NIc)
7d: NICKEL (II) ION (NId)
8a: IRON/SULFUR CLUSTER (SF4a)
8b: IRON/SULFUR CLUSTER (SF4b)
8c: IRON/SULFUR CLUSTER (SF4c)
8d: IRON/SULFUR CLUSTER (SF4d)
8e: IRON/SULFUR CLUSTER (SF4e)
8f: IRON/SULFUR CLUSTER (SF4f)
8g: IRON/SULFUR CLUSTER (SF4g)
8h: IRON/SULFUR CLUSTER (SF4h)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
-1
Ligand/Ion
CHLORIDE ION
2
F4S
1
Ligand/Ion
FE4-S3 CLUSTER
3
FCO
1
Ligand/Ion
CARBONMONOXIDE-(DICYANO) IRON
4
HEM
-1
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
5
LMT
-1
Ligand/Ion
DODECYL-BETA-D-MALTOSIDE
6
MG
-1
Ligand/Ion
MAGNESIUM ION
7
NI
-1
Ligand/Ion
NICKEL (II) ION
8
SF4
2
Ligand/Ion
IRON/SULFUR CLUSTER
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Sites
(10, 10)
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: BC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS S:187 , CYS S:190 , ARG S:192 , ARG S:193 , CYS S:215 , LEU S:216 , TYR S:217 , CYS S:221 , PRO S:224 , ILE S:243
BINDING SITE FOR RESIDUE SF4 S 401
02
AC2
SOFTWARE
THR S:226 , CYS S:230 , TRP S:235 , CYS S:242 , CYS S:249 , LEU S:250 , CYS S:252
BINDING SITE FOR RESIDUE SF4 S 402
03
AC3
SOFTWARE
HIS L:229 , CYS S:17 , THR S:18 , CYS S:19 , CYS S:20 , THR S:114 , CYS S:115 , CYS S:120 , CYS S:149
BINDING SITE FOR RESIDUE F4S S 403
04
AC4
SOFTWARE
TRP S:118 , GLY S:119 , CYS S:120 , GLY S:256
BINDING SITE FOR RESIDUE CL S 404
05
AC5
SOFTWARE
LEU M:259 , HIS S:29 , ASP S:237
BINDING SITE FOR RESIDUE CL S 405
06
AC6
SOFTWARE
CYS L:79 , VAL L:82 , HIS L:83 , ALA L:507 , PRO L:508 , ARG L:509 , LEU L:512 , VAL L:530 , PRO L:531 , THR L:532 , CYS L:579 , NI L:602
BINDING SITE FOR RESIDUE FCO L 601
07
AC7
SOFTWARE
CYS L:76 , CYS L:79 , CYS L:576 , CYS L:579 , FCO L:601
BINDING SITE FOR RESIDUE NI L 602
08
AC8
SOFTWARE
GLU L:57 , CYS L:528 , HIS L:582 , HOH L:701 , HOH L:702 , HOH L:703
BINDING SITE FOR RESIDUE MG L 603
09
AC9
SOFTWARE
PHE L:212 , ARG L:266
BINDING SITE FOR RESIDUE CL L 604
10
BC9
SOFTWARE
ILE M:243 , ASN M:253 , MET M:254 , MET S:180
BINDING SITE FOR RESIDUE CL M 605
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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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PROSITE Patterns/Profiles
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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.
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SCOP Domains
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CATH Domains
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Pfam Domains
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Asymmetric Unit 1
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Show PDB file:
Asym.Unit (1.3 MB)
Header - Asym.Unit
Biol.Unit 1 (674 KB)
Header - Biol.Unit 1
Biol.Unit 2 (312 KB)
Header - Biol.Unit 2
Biol.Unit 3 (374 KB)
Header - Biol.Unit 3
Biol.Unit 4 (674 KB)
Header - Biol.Unit 4
Biol.Unit 5 (311 KB)
Header - Biol.Unit 5
Biol.Unit 6 (375 KB)
Header - Biol.Unit 6
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