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1KSI
Asym. Unit
Info
Asym.Unit (230 KB)
Biol.Unit 1 (223 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF A EUKARYOTIC (PEA SEEDLING) COPPER-CONTAINING AMINE OXIDASE AT 2.2A RESOLUTION
Authors
:
M. C. J. Wilce, V. Kumar, H. C. Freeman, J. M. Guss
Date
:
20 Jul 96 (Deposition) - 24 Dec 97 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Oxidase, Pea Seedling, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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)
Reference
:
V. Kumar, D. M. Dooley, H. C. Freeman, J. M. Guss, I. Harvey, M. A. Mcguirl, M. C. Wilce, V. M. Zubak
Crystal Structure Of A Eukaryotic (Pea Seedling) Copper-Containing Amine Oxidase At 2. 2 A Resolution.
Structure V. 4 943 1996
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Hetero Components
(4, 12)
Info
All Hetero Components
1a: COPPER (II) ION (CUa)
1b: COPPER (II) ION (CUb)
2a: MANGANESE (II) ION (MNa)
2b: MANGANESE (II) ION (MNb)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
3d: N-ACETYL-D-GLUCOSAMINE (NAGd)
3e: N-ACETYL-D-GLUCOSAMINE (NAGe)
3f: N-ACETYL-D-GLUCOSAMINE (NAGf)
4a: 5-(2-CARBOXY-2-AMINOETHYL)-2-HYDRO... (TPQa)
4b: 5-(2-CARBOXY-2-AMINOETHYL)-2-HYDRO... (TPQb)
View:
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Label:
No.
Name
Count
Type
Full Name
1
CU
2
Ligand/Ion
COPPER (II) ION
2
MN
2
Ligand/Ion
MANGANESE (II) ION
3
NAG
6
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
TPQ
2
Mod. Amino Acid
5-(2-CARBOXY-2-AMINOETHYL)-2-HYDROXY-1,4-BENZOQUINONE
[
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Sites
(12, 12)
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: ACA (UNKNOWN)
11: ACB (UNKNOWN)
12: BC1 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:131 , SER A:133 , GLU A:134 , NAG A:656
BINDING SITE FOR RESIDUE NAG A 655
02
AC2
SOFTWARE
NAG A:655
BINDING SITE FOR RESIDUE NAG A 656
03
AC3
SOFTWARE
ASN A:558 , THR A:560 , GLU A:561 , GLN A:584
BINDING SITE FOR RESIDUE NAG A 657
04
AC4
SOFTWARE
ASN B:131 , SER B:133 , GLU B:134 , NAG B:656
BINDING SITE FOR RESIDUE NAG B 655
05
AC5
SOFTWARE
NAG B:655
BINDING SITE FOR RESIDUE NAG B 656
06
AC6
SOFTWARE
ASN B:558 , THR B:560 , GLU B:561 , GLN B:584
BINDING SITE FOR RESIDUE NAG B 657
07
AC7
SOFTWARE
HIS A:442 , HIS A:444 , HIS A:603 , HOH A:658 , HOH A:659
BINDING SITE FOR RESIDUE CU A 650
08
AC8
SOFTWARE
ASP A:451 , PHE A:452 , ASP A:453 , ASP A:592 , ILE A:593 , HOH A:660
BINDING SITE FOR RESIDUE MN A 653
09
AC9
SOFTWARE
HIS B:442 , HIS B:444 , HIS B:603 , HOH B:658 , HOH B:659
BINDING SITE FOR RESIDUE CU B 650
10
ACA
UNKNOWN
HIS A:442 , HIS A:444 , HIS A:603 , CU A:650 , HOH A:658 , HOH A:659 , TPQ A:387
THE COPPER ATOM IN THE ACTIVE SITE OF EACH SUBUNIT IS LIGATED TO THREE HISTIDINE RESIDUES AND TWO WATER MOLECULES IN A DISTORTED SQUARE PYRAMIDAL ARRANGEMENT. THE ORGANIC COFACTOR TOPA QUINONE (TPQ) IS IN THE ACTIVE SITE WITH THE NEAREST QUINONE OXYGEN ATOM AT ~6A FROM THE COPPER ATOM.
11
ACB
UNKNOWN
HIS B:442 , HIS B:444 , HIS B:603 , CU B:650 , HOH B:658 , HOH B:659 , TPQ B:387
THE COPPER ATOM IN THE ACTIVE SITE OF EACH SUBUNIT IS LIGATED TO THREE HISTIDINE RESIDUES AND TWO WATER MOLECULES IN A DISTORTED SQUARE PYRAMIDAL ARRANGEMENT. THE ORGANIC COFACTOR TOPA QUINONE (TPQ) IS IN THE ACTIVE SITE WITH THE NEAREST QUINONE OXYGEN ATOM AT ~6A FROM THE COPPER ATOM.
12
BC1
SOFTWARE
ASP B:451 , PHE B:452 , ASP B:453 , ASP B:592 , ILE B:593 , HOH B:660
BINDING SITE FOR RESIDUE MN B 653
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: COPPER_AMINE_OXID_1 (A:376-389,B:376-389)
;
View:
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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_PEA
401-414
2
A:376-389
B:376-389
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Exons
(0, 0)
Info
All Exons
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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
(2, 6)
Info
All SCOP Domains
1a: SCOP_d1ksia1 (A:207-647)
1b: SCOP_d1ksib1 (B:207-647)
2a: SCOP_d1ksia2 (A:6-98)
2b: SCOP_d1ksib2 (B:6-98)
2c: SCOP_d1ksib3 (B:99-206)
2d: SCOP_d1ksia3 (A:99-206)
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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)
Pea (Pisum sativum) [TaxId: 3888]
(2)
1a
d1ksia1
A:207-647
1b
d1ksib1
B:207-647
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)
Pea (Pisum sativum) [TaxId: 3888]
(2)
2a
d1ksia2
A:6-98
2b
d1ksib2
B:6-98
2c
d1ksib3
B:99-206
2d
d1ksia3
A:99-206
[
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CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_1ksiA01 (A:6-101)
1b: CATH_1ksiB01 (B:6-101)
1c: CATH_1ksiA02 (A:102-197)
1d: CATH_1ksiB02 (B:102-197)
2a: CATH_1ksiA03 (A:231-646)
2b: CATH_1ksiB03 (B:231-646)
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)
Organisms
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)
Class
:
Alpha Beta
(26913)
Architecture
:
Roll
(3276)
Topology
:
Nuclear Transport Factor 2; Chain: A,
(517)
Homologous Superfamily
:
[code=3.10.450.40, no name defined]
(77)
Pea (Pisum sativum)
(2)
1a
1ksiA01
A:6-101
1b
1ksiB01
B:6-101
1c
1ksiA02
A:102-197
1d
1ksiB02
B:102-197
Class
:
Mainly Beta
(13760)
Architecture
:
Distorted Sandwich
(506)
Topology
:
Beta-galactosidase; Chain A, domain 5
(250)
Homologous Superfamily
:
Copper amine oxidase, Domain 3
(74)
Pea (Pisum sativum)
(2)
2a
1ksiA03
A:231-646
2b
1ksiB03
B:231-646
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Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_Cu_amine_oxidN2_1ksiB01 (B:8-95)
1b: PFAM_Cu_amine_oxidN2_1ksiB02 (B:8-95)
2a: PFAM_Cu_amine_oxidN3_1ksiB03 (B:101-198)
2b: PFAM_Cu_amine_oxidN3_1ksiB04 (B:101-198)
3a: PFAM_Cu_amine_oxid_1ksiB05 (B:220-641)
3b: PFAM_Cu_amine_oxid_1ksiB06 (B:220-641)
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Clans
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)
Organisms
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)
Clan
:
CuAO_N2_N3
(40)
Family
:
Cu_amine_oxidN2
(27)
Pisum sativum (Garden pea)
(2)
1a
Cu_amine_oxidN2-1ksiB01
B:8-95
1b
Cu_amine_oxidN2-1ksiB02
B:8-95
Family
:
Cu_amine_oxidN3
(37)
Pisum sativum (Garden pea)
(2)
2a
Cu_amine_oxidN3-1ksiB03
B:101-198
2b
Cu_amine_oxidN3-1ksiB04
B:101-198
Clan
:
no clan defined [family: Cu_amine_oxid]
(40)
Family
:
Cu_amine_oxid
(40)
Pisum sativum (Garden pea)
(2)
3a
Cu_amine_oxid-1ksiB05
B:220-641
3b
Cu_amine_oxid-1ksiB06
B:220-641
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