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3DE8
Biol. Unit 1
Info
Asym.Unit (87 KB)
Biol.Unit 1 (80 KB)
Biol.Unit 2 (42 KB)
Biol.Unit 3 (42 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF A DIMERIC CYTOCHROME CB562 ASSEMBLY INDUCED BY COPPER COORDINATION
Authors
:
E. N. Salgado, R. A. Lewis, A. L. Rheingold, F. A. Tezcan
Date
:
08 Jun 08 (Deposition) - 21 Apr 09 (Release) - 21 Apr 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.72
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: B,C (1x)
Biol. Unit 3: A,D (1x)
Keywords
:
Cu-Stabilized Dimeric Superstructure, Electron Transport, Heme, Iron, Metal-Binding, Periplasm, Transport, Metal Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. N. Salgado, R. A. Lewis, S. Mossin, A. L. Rheingold, F. A. Tezcan
Control Of Protein Oligomerization Symmetry By Metal Coordination: C2 And C3 Symmetrical Assemblies Through Cu(Ii) And Ni(Ii) Coordination.
Inorg. Chem. V. 48 2726 2009
(for further references see the
PDB file header
)
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Hetero Components
(1, 4)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
2a: COPPER (II) ION (CUa)
2b: COPPER (II) ION (CUb)
2c: COPPER (II) ION (CUc)
2d: COPPER (II) ION (CUd)
3a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
3b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
3c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
3d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
CU
-1
Ligand/Ion
COPPER (II) ION
3
HEM
4
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
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Sites
(14, 14)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:59 , HIS A:63 , HIS D:73 , HIS D:77 , HOH D:151
BINDING SITE FOR RESIDUE CU A 107
02
AC2
SOFTWARE
HIS A:73 , HIS A:77 , HIS D:59 , HIS D:63 , HOH D:152
BINDING SITE FOR RESIDUE CU A 108
03
AC3
SOFTWARE
ASP A:74 , HOH A:151 , HOH A:152 , ASP C:74 , HOH C:313 , HOH C:314
BINDING SITE FOR RESIDUE CA A 109
04
AC4
SOFTWARE
GLU A:8 , ASP A:12 , HOH A:153 , HOH A:154 , HOH A:155
BINDING SITE FOR RESIDUE CA A 110
05
AC5
SOFTWARE
HOH A:200 , HOH A:217 , HOH A:228 , HOH A:278 , HOH A:292
BINDING SITE FOR RESIDUE CA A 111
06
AC6
SOFTWARE
HIS B:59 , HIS B:63 , HIS C:73 , HIS C:77 , HOH C:312
BINDING SITE FOR RESIDUE CU B 107
07
AC7
SOFTWARE
HIS B:73 , HIS B:77 , HOH B:253 , HIS C:59 , HIS C:63
BINDING SITE FOR RESIDUE CU B 108
08
AC8
SOFTWARE
ALA A:1 , ASP A:39 , GLU B:4 , ASP B:5 , HOH B:254 , HOH B:255
BINDING SITE FOR RESIDUE CA B 109
09
AC9
SOFTWARE
ASP A:39 , ASP B:2 , GLU B:4 , ASP B:5 , HOH B:256 , HOH B:257
BINDING SITE FOR RESIDUE CA B 110
10
BC1
SOFTWARE
LYS C:19 , ASP C:21 , HOH C:315 , HOH C:316
BINDING SITE FOR RESIDUE CA C 107
11
BC2
SOFTWARE
MET A:7 , MET A:33 , PRO A:45 , PRO A:46 , PHE A:61 , PHE A:65 , CYS A:98 , CYS A:101 , HIS A:102 , ARG A:106 , HOH A:258 , HOH A:301
BINDING SITE FOR RESIDUE HEM A 150
12
BC3
SOFTWARE
ALA A:1 , HOH A:294 , LEU B:3 , MET B:7 , GLU B:8 , PRO B:45 , PRO B:46 , PHE B:61 , PHE B:65 , CYS B:98 , CYS B:101 , HIS B:102 , TYR B:105 , ARG B:106 , HOH B:264
BINDING SITE FOR RESIDUE HEM B 150
13
BC4
SOFTWARE
GLU C:4 , MET C:7 , PRO C:45 , PRO C:46 , PHE C:61 , PHE C:65 , CYS C:98 , CYS C:101 , HIS C:102 , TYR C:105 , ARG C:106 , HOH C:331 , HOH C:342 , HOH C:404 , HOH C:429
BINDING SITE FOR RESIDUE HEM C 150
14
BC5
SOFTWARE
GLU D:4 , MET D:7 , GLU D:8 , PRO D:45 , PRO D:46 , PHE D:61 , GLY D:64 , PHE D:65 , CYS D:98 , CYS D:101 , HIS D:102 , TYR D:105 , ARG D:106 , HOH D:218
BINDING SITE FOR RESIDUE HEM D 150
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d3de8a_ (A:)
1b: SCOP_d3de8b_ (B:)
1c: SCOP_d3de8c_ (C:)
1d: SCOP_d3de8d_ (D:)
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(
)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Four-helical up-and-down bundle
(308)
Superfamily
:
Cytochromes
(82)
Family
:
Cytochrome b562
(38)
Protein domain
:
automated matches
(32)
Escherichia coli [TaxId: 562]
(31)
1a
d3de8a_
A:
1b
d3de8b_
B:
1c
d3de8c_
C:
1d
d3de8d_
D:
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_3de8A00 (A:1-106)
1b: CATH_3de8B00 (B:1-106)
1c: CATH_3de8C00 (C:1-106)
1d: CATH_3de8D00 (D:1-106)
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(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Four Helix Bundle (Hemerythrin (Met), subunit A)
(300)
Homologous Superfamily
:
[code=1.20.120.10, no name defined]
(45)
Escherichia coli. Organism_taxid: 562.
(13)
1a
3de8A00
A:1-106
1b
3de8B00
B:1-106
1c
3de8C00
C:1-106
1d
3de8D00
D:1-106
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Pfam Domains
(0, 0)
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Asymmetric Unit 1
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select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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Show PDB file:
Asym.Unit (87 KB)
Header - Asym.Unit
Biol.Unit 1 (80 KB)
Header - Biol.Unit 1
Biol.Unit 2 (42 KB)
Header - Biol.Unit 2
Biol.Unit 3 (42 KB)
Header - Biol.Unit 3
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