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3DE8
Asym. Unit
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
(3, 14)
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
6
Ligand/Ion
CALCIUM ION
2
CU
4
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 not available)
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PROSITE Patterns/Profiles
(0, 0)
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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.
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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(
)
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'
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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
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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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