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2W0Q
Asym. Unit
Info
Asym.Unit (249 KB)
Biol.Unit 1 (242 KB)
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(1)
Title
:
E. COLI COPPER AMINE OXIDASE IN COMPLEX WITH XENON
Authors
:
P. Pirrat, M. A. Smith, A. R. Pearson, M. J. Mcpherson, S. E. V. Phillips
Date
:
20 Aug 08 (Deposition) - 16 Dec 08 (Release) - 23 Dec 08 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.48
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Tpq, Xenon, Copper, E. Coli, Calcium, Periplasm, Oxygen Entry, Metal-Binding, Oxidoreductase, Copper Amine Oxidase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Pirrat, M. A. Smith, A. R. Pearson, M. J. Mcpherson, S. E. V. Phillips
Structure Of A Xenon Derivative Of Escherichia Coli Copper Amine Oxidase: Confirmation Of The Proposed Oxygen-Entry Pathway.
Acta Crystallogr. , Sect. F V. 64 1105 2008
[
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Hetero Components
(4, 19)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: COPPER (II) ION (CUa)
2b: COPPER (II) ION (CUb)
3a: 5-(2-CARBOXY-2-AMINOETHYL)-2-HYDRO... (TPQa)
3b: 5-(2-CARBOXY-2-AMINOETHYL)-2-HYDRO... (TPQb)
4a: XENON (XEa)
4b: XENON (XEb)
4c: XENON (XEc)
4d: XENON (XEd)
4e: XENON (XEe)
4f: XENON (XEf)
4g: XENON (XEg)
4h: XENON (XEh)
4i: XENON (XEi)
4j: XENON (XEj)
4k: XENON (XEk)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
4
Ligand/Ion
CALCIUM ION
2
CU
2
Ligand/Ion
COPPER (II) ION
3
TPQ
2
Mod. Amino Acid
5-(2-CARBOXY-2-AMINOETHYL)-2-HYDROXY-1,4-BENZOQUINONE
4
XE
11
Ligand/Ion
XENON
[
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Sites
(17, 17)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:524 , HIS A:526 , HIS A:689 , HOH A:2226
BINDING SITE FOR RESIDUE CU A 801
02
AC2
SOFTWARE
LYS A:133 , ASP A:533 , LEU A:534 , ASP A:535 , ASP A:678 , ALA A:679 , HOH A:2254
BINDING SITE FOR RESIDUE CA A 802
03
AC3
SOFTWARE
GLU A:573 , TYR A:667 , GLU A:672 , HOH A:2290 , HOH A:2294
BINDING SITE FOR RESIDUE CA A 803
04
AC4
SOFTWARE
PHE A:192 , TYR A:387
BINDING SITE FOR RESIDUE XE A 901
05
AC5
SOFTWARE
PHE A:330
BINDING SITE FOR RESIDUE XE A 903
06
AC6
SOFTWARE
TYR A:381
BINDING SITE FOR RESIDUE XE A 904
07
AC7
SOFTWARE
LEU A:543 , ALA A:576 , GLN A:578 , LEU A:638
BINDING SITE FOR RESIDUE XE A 907
08
AC8
SOFTWARE
SER A:394 , ILE A:396 , ALA A:426 , ILE A:460
BINDING SITE FOR RESIDUE XE A 908
09
AC9
SOFTWARE
LEU A:543 , ILE A:605
BINDING SITE FOR RESIDUE XE A 909
10
BC1
SOFTWARE
HIS B:524 , HIS B:526 , HIS B:689
BINDING SITE FOR RESIDUE CU B 801
11
BC2
SOFTWARE
LYS B:133 , ASP B:533 , LEU B:534 , ASP B:535 , ASP B:678 , ALA B:679 , HOH B:2204
BINDING SITE FOR RESIDUE CA B 802
12
BC3
SOFTWARE
GLU B:573 , TYR B:667 , GLU B:672 , HOH B:2232
BINDING SITE FOR RESIDUE CA B 803
13
BC4
SOFTWARE
VAL B:187 , PHE B:192 , TYR B:387
BINDING SITE FOR RESIDUE XE B 902
14
BC5
SOFTWARE
LEU B:543 , ALA B:576 , GLN B:578 , LEU B:638
BINDING SITE FOR RESIDUE XE B 905
15
BC6
SOFTWARE
PHE B:330
BINDING SITE FOR RESIDUE XE B 906
16
BC7
SOFTWARE
PRO A:548 , VAL A:549 , MET A:563 , GLN B:620
BINDING SITE FOR RESIDUE XE B 910
17
BC8
SOFTWARE
THR B:223 , TYR B:381 , TYR B:387
BINDING SITE FOR RESIDUE XE B 911
[
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SAPs(SNPs)/Variants
(2, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_AMO_ECOLI_001 (K12E, chain A/B, )
2: VAR_AMO_ECOLI_002 (L29I, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_AMO_ECOLI_001
*
K
42
E
AMO_ECOLI
---
---
A/B
K
12
E
2
UniProt
VAR_AMO_ECOLI_002
*
L
59
I
AMO_ECOLI
---
---
A/B
L
29
I
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: COPPER_AMINE_OXID_1 (A:455-468,B:455-468)
2: COPPER_AMINE_OXID_2 (A:684-697,B:684-697)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
COPPER_AMINE_OXID_1
PS01164
Copper amine oxidase topaquinone signature.
AMO_ECOLI
485-498
2
A:455-468
B:455-468
2
COPPER_AMINE_OXID_2
PS01165
Copper amine oxidase copper-binding site signature.
AMO_ECOLI
714-727
2
A:684-697
B:684-697
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(3, 8)
Info
All SCOP Domains
1a: SCOP_d2w0qa4 (A:301-725)
1b: SCOP_d2w0qb4 (B:301-726)
2a: SCOP_d2w0qa2 (A:91-185)
2b: SCOP_d2w0qa3 (A:186-300)
2c: SCOP_d2w0qb2 (B:91-185)
2d: SCOP_d2w0qb3 (B:186-300)
3a: SCOP_d2w0qa1 (A:7-90)
3b: SCOP_d2w0qb1 (B:6-90)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Supersandwich
(271)
Superfamily
:
Amine oxidase catalytic domain
(65)
Family
:
Amine oxidase catalytic domain
(65)
Protein domain
:
Copper amine oxidase, domain 3
(62)
Escherichia coli [TaxId: 562]
(16)
1a
d2w0qa4
A:301-725
1b
d2w0qb4
B:301-726
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Cystatin-like
(403)
Superfamily
:
Amine oxidase N-terminal region
(65)
Family
:
Amine oxidase N-terminal region
(65)
Protein domain
:
Copper amine oxidase, domains 1 and 2
(62)
Escherichia coli [TaxId: 562]
(16)
2a
d2w0qa2
A:91-185
2b
d2w0qa3
A:186-300
2c
d2w0qb2
B:91-185
2d
d2w0qb3
B:186-300
Fold
:
N domain of copper amine oxidase-like
(44)
Superfamily
:
Copper amine oxidase, domain N
(16)
Family
:
Copper amine oxidase, domain N
(16)
Protein domain
:
Copper amine oxidase, domain N
(16)
Escherichia coli [TaxId: 562]
(16)
3a
d2w0qa1
A:7-90
3b
d2w0qb1
B:6-90
[
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CATH Domains
(3, 8)
Info
all CATH domains
1a: CATH_2w0qB01 (B:6-84)
1b: CATH_2w0qA01 (A:7-84)
2a: CATH_2w0qA02 (A:86-186)
2b: CATH_2w0qA03 (A:187-292)
2c: CATH_2w0qB03 (B:187-292)
2d: CATH_2w0qB02 (B:86-186)
3a: CATH_2w0qA04 (A:314-723)
3b: CATH_2w0qB04 (B:314-723)
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(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Copper Amine Oxidase; Chain A, domain 1
(16)
Homologous Superfamily
:
[code=3.30.457.10, no name defined]
(16)
Escherichia coli. Organism_taxid: 562.
(8)
1a
2w0qB01
B:6-84
1b
2w0qA01
A:7-84
Architecture
:
Roll
(3276)
Topology
:
Nuclear Transport Factor 2; Chain: A,
(517)
Homologous Superfamily
:
[code=3.10.450.40, no name defined]
(77)
Escherichia coli. Organism_taxid: 562.
(8)
2a
2w0qA02
A:86-186
2b
2w0qA03
A:187-292
2c
2w0qB03
B:187-292
2d
2w0qB02
B:86-186
Class
:
Mainly Beta
(13760)
Architecture
:
Distorted Sandwich
(506)
Topology
:
Beta-galactosidase; Chain A, domain 5
(250)
Homologous Superfamily
:
Copper amine oxidase, Domain 3
(74)
Escherichia coli. Organism_taxid: 562.
(8)
3a
2w0qA04
A:314-723
3b
2w0qB04
B:314-723
[
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Pfam Domains
(4, 8)
Info
all PFAM domains
1a: PFAM_Cu_amine_oxidN2_2w0qB01 (B:94-180)
1b: PFAM_Cu_amine_oxidN2_2w0qB02 (B:94-180)
2a: PFAM_Cu_amine_oxidN3_2w0qB03 (B:185-287)
2b: PFAM_Cu_amine_oxidN3_2w0qB04 (B:185-287)
3a: PFAM_Cu_amine_oxidN1_2w0qB05 (B:6-91)
3b: PFAM_Cu_amine_oxidN1_2w0qB06 (B:6-91)
4a: PFAM_Cu_amine_oxid_2w0qB07 (B:305-726)
4b: PFAM_Cu_amine_oxid_2w0qB08 (B:305-726)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
CuAO_N2_N3
(40)
Family
:
Cu_amine_oxidN2
(27)
Escherichia coli (strain K12)
(12)
1a
Cu_amine_oxidN2-2w0qB01
B:94-180
1b
Cu_amine_oxidN2-2w0qB02
B:94-180
Family
:
Cu_amine_oxidN3
(37)
Escherichia coli (strain K12)
(12)
2a
Cu_amine_oxidN3-2w0qB03
B:185-287
2b
Cu_amine_oxidN3-2w0qB04
B:185-287
Clan
:
no clan defined [family: Cu_amine_oxidN1]
(12)
Family
:
Cu_amine_oxidN1
(12)
Escherichia coli (strain K12)
(12)
3a
Cu_amine_oxidN1-2w0qB05
B:6-91
3b
Cu_amine_oxidN1-2w0qB06
B:6-91
Clan
:
no clan defined [family: Cu_amine_oxid]
(40)
Family
:
Cu_amine_oxid
(40)
Escherichia coli (strain K12)
(12)
4a
Cu_amine_oxid-2w0qB07
B:305-726
4b
Cu_amine_oxid-2w0qB08
B:305-726
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