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2OOV
Biol. Unit 2
Info
Asym.Unit (741 KB)
Biol.Unit 1 (250 KB)
Biol.Unit 2 (251 KB)
Biol.Unit 3 (251 KB)
Biol.Unit 4 (730 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HANSENULA POLYMORPHA AMINE OXIDASE TO 1.7 ANGSTROMS
Authors
:
B. J. Johnson, C. M. Wilmot
Date
:
26 Jan 07 (Deposition) - 10 Apr 07 (Release) - 18 Apr 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Biol. Unit 4: A,B,C,D,E,F (1x)
Keywords
:
Protein-Derived Cofactor, Beta-Sandwich, Tpq, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. J. Johnson, J. Cohen, R. W. Welford, A. R. Pearson, K. Schulten, J. P. Klinman, C. M. Wilmot
Exploring Molecular Oxygen Pathways In Hansenula Polymorpha Copper-Containing Amine Oxidase
J. Biol. Chem. V. 282 17767 2007
[
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Hetero Components
(3, 9)
Info
All Hetero Components
1a: COPPER (II) ION (CUa)
1b: COPPER (II) ION (CUb)
1c: COPPER (II) ION (CUc)
1d: COPPER (II) ION (CUd)
1e: COPPER (II) ION (CUe)
1f: COPPER (II) ION (CUf)
2a: GLYCEROL (GOLa)
2aa: GLYCEROL (GOLaa)
2ab: GLYCEROL (GOLab)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
2i: GLYCEROL (GOLi)
2j: GLYCEROL (GOLj)
2k: GLYCEROL (GOLk)
2l: GLYCEROL (GOLl)
2m: GLYCEROL (GOLm)
2n: GLYCEROL (GOLn)
2o: GLYCEROL (GOLo)
2p: GLYCEROL (GOLp)
2q: GLYCEROL (GOLq)
2r: GLYCEROL (GOLr)
2s: GLYCEROL (GOLs)
2t: GLYCEROL (GOLt)
2u: GLYCEROL (GOLu)
2v: GLYCEROL (GOLv)
2w: GLYCEROL (GOLw)
2x: GLYCEROL (GOLx)
2y: GLYCEROL (GOLy)
2z: GLYCEROL (GOLz)
3a: PHOSPHATE ION (PO4a)
3b: PHOSPHATE ION (PO4b)
4a: METHIONINE SULFOXIDE (SMEa)
4b: METHIONINE SULFOXIDE (SMEb)
5a: 5-(2-CARBOXY-2-AMINOETHYL)-2-HYDRO... (TPQa)
5b: 5-(2-CARBOXY-2-AMINOETHYL)-2-HYDRO... (TPQb)
5c: 5-(2-CARBOXY-2-AMINOETHYL)-2-HYDRO... (TPQc)
5d: 5-(2-CARBOXY-2-AMINOETHYL)-2-HYDRO... (TPQd)
5e: 5-(2-CARBOXY-2-AMINOETHYL)-2-HYDRO... (TPQe)
5f: 5-(2-CARBOXY-2-AMINOETHYL)-2-HYDRO... (TPQf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CU
-1
Ligand/Ion
COPPER (II) ION
2
GOL
6
Ligand/Ion
GLYCEROL
3
PO4
1
Ligand/Ion
PHOSPHATE ION
4
SME
-1
Mod. Amino Acid
METHIONINE SULFOXIDE
5
TPQ
2
Mod. Amino Acid
5-(2-CARBOXY-2-AMINOETHYL)-2-HYDROXY-1,4-BENZOQUINONE
[
close Hetero Component info
]
Sites
(11, 11)
Info
All Sites
01: AC3 (SOFTWARE)
02: AC4 (SOFTWARE)
03: AC7 (SOFTWARE)
04: BC1 (SOFTWARE)
05: BC6 (SOFTWARE)
06: CC9 (SOFTWARE)
07: DC2 (SOFTWARE)
08: DC4 (SOFTWARE)
09: DC7 (SOFTWARE)
10: DC8 (SOFTWARE)
11: DC9 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC3
SOFTWARE
TPQ C:405 , HIS C:456 , HIS C:458 , HIS C:624
BINDING SITE FOR RESIDUE CU C 801
02
AC4
SOFTWARE
TPQ D:405 , LEU D:425 , HIS D:456 , HIS D:458 , HIS D:624 , HOH D:6751
BINDING SITE FOR RESIDUE CU D 801
03
AC7
SOFTWARE
HIS C:218 , LYS C:219 , HOH C:6697 , HOH C:6762 , HOH C:6767
BINDING SITE FOR RESIDUE PO4 C 6010
04
BC1
SOFTWARE
LYS C:214 , VAL C:215 , ASP C:436 , HOH C:6215 , HOH C:6429 , HOH C:6812
BINDING SITE FOR RESIDUE GOL C 6002
05
BC6
SOFTWARE
LYS C:393 , VAL C:412 , ASP C:422 , ARG C:424 , HOH C:6164 , HOH C:6785 , HOH C:6873
BINDING SITE FOR RESIDUE GOL C 6007
06
CC9
SOFTWARE
HIS C:286 , PHE C:649 , THR C:650 , GLU C:651 , PRO C:653 , GOL C:6029 , HOH C:6125 , HOH C:6181 , HOH C:6294 , HOH C:6530
BINDING SITE FOR RESIDUE GOL C 6021
07
DC2
SOFTWARE
GLY B:142 , PRO B:144 , GLU B:147 , TYR B:177 , HOH B:6704 , HOH D:6484
BINDING SITE FOR RESIDUE GOL B 6023
08
DC4
SOFTWARE
GLY B:603 , ASP B:604 , HOH B:6375 , HOH B:6599 , PRO D:490 , GLU D:491
BINDING SITE FOR RESIDUE GOL B 6025
09
DC7
SOFTWARE
ARG D:20 , PRO D:21 , LEU D:74 , PRO D:75 , ARG D:77 , HOH D:6304 , HOH D:6372 , HOH D:6662 , HOH D:6867
BINDING SITE FOR RESIDUE GOL D 6028
10
DC8
SOFTWARE
GLN B:66 , GLN B:70 , GLY B:72 , TYR C:534 , THR C:650 , GLU C:651 , GOL C:6021 , HOH C:6076 , HOH C:6530 , TYR D:448
BINDING SITE FOR RESIDUE GOL C 6029
11
DC9
SOFTWARE
GLY C:371 , LYS D:393 , VAL D:412 , ARG D:420 , ASP D:422 , ARG D:424 , HOH D:6088 , HOH D:6516 , HOH D:6744 , HOH D:6769
BINDING SITE FOR RESIDUE GOL D 6030
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: COPPER_AMINE_OXID_1 (C:394-407,D:394-407)
2: COPPER_AMINE_OXID_2 (C:619-632,D:619-632)
;
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_PICAN
394-407
2
-
-
C:394-407
D:394-407
-
-
2
COPPER_AMINE_OXID_2
PS01165
Copper amine oxidase copper-binding site signature.
AMO_PICAN
619-632
2
-
-
C:619-632
D:619-632
-
-
[
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]
Exons
(0, 0)
Info
All Exons
View:
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 18)
Info
All SCOP Domains
1a: SCOP_d2oova1 (A:237-672)
1b: SCOP_d2oove1 (E:237-672)
1c: SCOP_d2oovf1 (F:237-672)
1d: SCOP_d2oovb1 (B:237-672)
1e: SCOP_d2oovc1 (C:237-672)
1f: SCOP_d2oovd1 (D:237-672)
2a: SCOP_d2oova2 (A:18-115)
2b: SCOP_d2oova3 (A:116-236)
2c: SCOP_d2oovb2 (B:18-115)
2d: SCOP_d2oovb3 (B:116-236)
2e: SCOP_d2oovc2 (C:18-115)
2f: SCOP_d2oovc3 (C:116-236)
2g: SCOP_d2oovd2 (D:18-115)
2h: SCOP_d2oovd3 (D:116-236)
2i: SCOP_d2oove2 (E:18-115)
2j: SCOP_d2oove3 (E:116-236)
2k: SCOP_d2oovf2 (F:18-115)
2l: SCOP_d2oovf3 (F:116-236)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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)
Yeast (Hansenula polymorpha) [TaxId: 4905]
(4)
1a
d2oova1
A:237-672
1b
d2oove1
E:237-672
1c
d2oovf1
F:237-672
1d
d2oovb1
B:237-672
1e
d2oovc1
C:237-672
1f
d2oovd1
D:237-672
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)
Yeast (Hansenula polymorpha) [TaxId: 4905]
(4)
2a
d2oova2
A:18-115
2b
d2oova3
A:116-236
2c
d2oovb2
B:18-115
2d
d2oovb3
B:116-236
2e
d2oovc2
C:18-115
2f
d2oovc3
C:116-236
2g
d2oovd2
D:18-115
2h
d2oovd3
D:116-236
2i
d2oove2
E:18-115
2j
d2oove3
E:116-236
2k
d2oovf2
F:18-115
2l
d2oovf3
F:116-236
[
close SCOP info
]
CATH Domains
(2, 18)
Info
all CATH domains
1a: CATH_2oovA01 (A:18-117)
1b: CATH_2oovE01 (E:18-117)
1c: CATH_2oovF01 (F:18-117)
1d: CATH_2oovA02 (A:123-231)
1e: CATH_2oovB02 (B:123-231)
1f: CATH_2oovC02 (C:123-231)
1g: CATH_2oovD02 (D:123-231)
1h: CATH_2oovE02 (E:123-231)
1i: CATH_2oovF02 (F:123-231)
1j: CATH_2oovB01 (B:18-117)
1k: CATH_2oovC01 (C:18-117)
1l: CATH_2oovD01 (D:18-117)
2a: CATH_2oovA03 (A:232-670)
2b: CATH_2oovE03 (E:232-670)
2c: CATH_2oovF03 (F:232-670)
2d: CATH_2oovB03 (B:232-670)
2e: CATH_2oovC03 (C:232-670)
2f: CATH_2oovD03 (D:232-670)
View:
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Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
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)
Pichia angusta. Organism_taxid: 4905.
(2)
1a
2oovA01
A:18-117
1b
2oovE01
E:18-117
1c
2oovF01
F:18-117
1d
2oovA02
A:123-231
1e
2oovB02
B:123-231
1f
2oovC02
C:123-231
1g
2oovD02
D:123-231
1h
2oovE02
E:123-231
1i
2oovF02
F:123-231
1j
2oovB01
B:18-117
1k
2oovC01
C:18-117
1l
2oovD01
D:18-117
Class
:
Mainly Beta
(13760)
Architecture
:
Distorted Sandwich
(506)
Topology
:
Beta-galactosidase; Chain A, domain 5
(250)
Homologous Superfamily
:
Copper amine oxidase, Domain 3
(74)
Pichia angusta. Organism_taxid: 4905.
(2)
2a
2oovA03
A:232-670
2b
2oovE03
E:232-670
2c
2oovF03
F:232-670
2d
2oovB03
B:232-670
2e
2oovC03
C:232-670
2f
2oovD03
D:232-670
[
close CATH info
]
Pfam Domains
(3, 18)
Info
all PFAM domains
1a: PFAM_Cu_amine_oxidN2_2oovF01 (F:23-109)
1b: PFAM_Cu_amine_oxidN2_2oovF02 (F:23-109)
1c: PFAM_Cu_amine_oxidN2_2oovF03 (F:23-109)
1d: PFAM_Cu_amine_oxidN2_2oovF04 (F:23-109)
1e: PFAM_Cu_amine_oxidN2_2oovF05 (F:23-109)
1f: PFAM_Cu_amine_oxidN2_2oovF06 (F:23-109)
2a: PFAM_Cu_amine_oxidN3_2oovF07 (F:114-216)
2b: PFAM_Cu_amine_oxidN3_2oovF08 (F:114-216)
2c: PFAM_Cu_amine_oxidN3_2oovF09 (F:114-216)
2d: PFAM_Cu_amine_oxidN3_2oovF10 (F:114-216)
2e: PFAM_Cu_amine_oxidN3_2oovF11 (F:114-216)
2f: PFAM_Cu_amine_oxidN3_2oovF12 (F:114-216)
3a: PFAM_Cu_amine_oxid_2oovF13 (F:241-662)
3b: PFAM_Cu_amine_oxid_2oovF14 (F:241-662)
3c: PFAM_Cu_amine_oxid_2oovF15 (F:241-662)
3d: PFAM_Cu_amine_oxid_2oovF16 (F:241-662)
3e: PFAM_Cu_amine_oxid_2oovF17 (F:241-662)
3f: PFAM_Cu_amine_oxid_2oovF18 (F:241-662)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
CuAO_N2_N3
(40)
Family
:
Cu_amine_oxidN2
(27)
Pichia angusta (Yeast) (Hansenula polymorpha)
(5)
1a
Cu_amine_oxidN2-2oovF01
F:23-109
1b
Cu_amine_oxidN2-2oovF02
F:23-109
1c
Cu_amine_oxidN2-2oovF03
F:23-109
1d
Cu_amine_oxidN2-2oovF04
F:23-109
1e
Cu_amine_oxidN2-2oovF05
F:23-109
1f
Cu_amine_oxidN2-2oovF06
F:23-109
Family
:
Cu_amine_oxidN3
(37)
Pichia angusta (Yeast) (Hansenula polymorpha)
(5)
2a
Cu_amine_oxidN3-2oovF07
F:114-216
2b
Cu_amine_oxidN3-2oovF08
F:114-216
2c
Cu_amine_oxidN3-2oovF09
F:114-216
2d
Cu_amine_oxidN3-2oovF10
F:114-216
2e
Cu_amine_oxidN3-2oovF11
F:114-216
2f
Cu_amine_oxidN3-2oovF12
F:114-216
Clan
:
no clan defined [family: Cu_amine_oxid]
(40)
Family
:
Cu_amine_oxid
(40)
Pichia angusta (Yeast) (Hansenula polymorpha)
(5)
3a
Cu_amine_oxid-2oovF13
F:241-662
3b
Cu_amine_oxid-2oovF14
F:241-662
3c
Cu_amine_oxid-2oovF15
F:241-662
3d
Cu_amine_oxid-2oovF16
F:241-662
3e
Cu_amine_oxid-2oovF17
F:241-662
3f
Cu_amine_oxid-2oovF18
F:241-662
[
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