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1D6Z
Asym. Unit
Info
Asym.Unit (267 KB)
Biol.Unit 1 (261 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE AEROBICALLY FREEZE TRAPPED RATE-DETERMINING CATALYTIC INTERMEDIATE OF E. COLI COPPER-CONTAINING AMINE OXIDASE.
Authors
:
C. M. Wilmot, J. Hajdu, M. J. Mcpherson, P. F. Knowles, S. E. V. Phillips
Date
:
16 Oct 99 (Deposition) - 02 Feb 00 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Reaction Intermediate, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. M. Wilmot, J. Hajdu, M. J. Mcpherson, P. F. Knowles, S. E. Phillips
Visualization Of Dioxygen Bound To Copper During Enzyme Catalysis.
Science V. 286 1724 1999
(for further references see the
PDB file header
)
[
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Hetero Components
(7, 15)
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: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
4a: PHENYLACETALDEHYDE (HY1a)
4b: PHENYLACETALDEHYDE (HY1b)
5a: 2-PHENYLETHYLAMINE (PEAa)
6a: HYDROGEN PEROXIDE (PEOa)
6b: HYDROGEN PEROXIDE (PEOb)
7a: 3-(4-HYDROXY-3-IMINO-6-OXO-CYCLOHE... (TYYa)
7b: 3-(4-HYDROXY-3-IMINO-6-OXO-CYCLOHE... (TYYb)
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
GOL
2
Ligand/Ion
GLYCEROL
4
HY1
2
Ligand/Ion
PHENYLACETALDEHYDE
5
PEA
1
Ligand/Ion
2-PHENYLETHYLAMINE
6
PEO
2
Ligand/Ion
HYDROGEN PEROXIDE
7
TYY
2
Mod. Amino Acid
3-(4-HYDROXY-3-IMINO-6-OXO-CYCLOHEXA-1,4-DIENYL)-ALANINE
[
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Sites
(13, 13)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:524 , HIS A:526 , HIS A:689 , PEO A:2002
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:2141
BINDING SITE FOR RESIDUE CA A 802
03
AC3
SOFTWARE
GLU A:573 , HIS A:644 , TYR A:667 , ASP A:670 , GLU A:672 , HOH A:2292
BINDING SITE FOR RESIDUE CA A 803
04
AC4
SOFTWARE
HIS B:524 , HIS B:526 , HIS B:689 , PEO B:3002
BINDING SITE FOR RESIDUE CU B 801
05
AC5
SOFTWARE
LYS B:133 , ASP B:533 , LEU B:534 , ASP B:535 , ASP B:678 , ALA B:679 , HOH B:3175
BINDING SITE FOR RESIDUE CA B 802
06
AC6
SOFTWARE
GLU B:573 , TYR B:667 , GLU B:672 , HOH B:3199 , HOH B:3203
BINDING SITE FOR RESIDUE CA B 803
07
AC7
SOFTWARE
PRO A:224 , LEU A:225 , TRP A:257 , TYR A:381 , ASP A:383 , TYR A:387 , VAL A:463 , GLY A:464 , TYY A:466
BINDING SITE FOR RESIDUE HY1 A 2001
08
AC8
SOFTWARE
TYY A:466 , GLU A:490 , HIS A:524 , HIS A:526 , CU A:801
BINDING SITE FOR RESIDUE PEO A 2002
09
AC9
SOFTWARE
GLN A:106 , LEU A:169 , HOH A:2747 , ALA B:56 , LEU B:57 , GLN B:58
BINDING SITE FOR RESIDUE PEA A 2003
10
BC1
SOFTWARE
LEU B:225 , TRP B:257 , TYR B:381 , ASP B:383 , TYR B:387 , VAL B:463 , GLY B:464 , TYY B:466
BINDING SITE FOR RESIDUE HY1 B 3001
11
BC2
SOFTWARE
TYY B:466 , GLU B:490 , HIS B:524 , HIS B:526 , CU B:801 , HOH B:3047
BINDING SITE FOR RESIDUE PEO B 3002
12
BC3
SOFTWARE
ARG A:452 , HIS A:475 , ASN A:477 , THR A:479 , LYS A:709 , THR B:612 , ARG B:692 , GLU B:702
BINDING SITE FOR RESIDUE GOL A 2004
13
BC4
SOFTWARE
ASP B:20 , SER B:404
BINDING SITE FOR RESIDUE GOL B 3003
[
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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)
[
close SNP/Variant info
]
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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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_d1d6za1 (A:301-724)
1b: SCOP_d1d6zb1 (B:301-725)
2a: SCOP_d1d6za2 (A:91-185)
2b: SCOP_d1d6zb2 (B:91-185)
2c: SCOP_d1d6zb3 (B:186-300)
2d: SCOP_d1d6za3 (A:186-300)
3a: SCOP_d1d6za4 (A:7-90)
3b: SCOP_d1d6zb4 (B:6-90)
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Protein Domains
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)
(
)
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
d1d6za1
A:301-724
1b
d1d6zb1
B:301-725
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
d1d6za2
A:91-185
2b
d1d6zb2
B:91-185
2c
d1d6zb3
B:186-300
2d
d1d6za3
A: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
d1d6za4
A:7-90
3b
d1d6zb4
B:6-90
[
close SCOP info
]
CATH Domains
(3, 8)
Info
all CATH domains
1a: CATH_1d6zB01 (B:6-84)
1b: CATH_1d6zA01 (A:7-84)
2a: CATH_1d6zA02 (A:86-186)
2b: CATH_1d6zB02 (B:86-186)
2c: CATH_1d6zA04 (A:187-292)
2d: CATH_1d6zB04 (B:187-292)
3a: CATH_1d6zA03 (A:314-723)
3b: CATH_1d6zB03 (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
1d6zB01
B:6-84
1b
1d6zA01
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
1d6zA02
A:86-186
2b
1d6zB02
B:86-186
2c
1d6zA04
A:187-292
2d
1d6zB04
B:187-292
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
1d6zA03
A:314-723
3b
1d6zB03
B:314-723
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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