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3NBJ
Asym. Unit
Info
Asym.Unit (690 KB)
Biol.Unit 1 (234 KB)
Biol.Unit 2 (234 KB)
Biol.Unit 3 (234 KB)
Biol.Unit 4 (681 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF Y305F MUTANT OF THE COPPER AMINE OXIDASE FROM HANSENULA POLYMORPHA EXPRESSED IN YEAST
Authors
:
Z. Chen, S. Datta, J. L. Dubois, J. P. Klinman, F. S. Mathews
Date
:
03 Jun 10 (Deposition) - 25 Aug 10 (Release) - 08 Sep 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
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
:
Amine Oxidase, Quinoprotein, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Z. W. Chen, S. Datta, J. L. Dubois, J. P. Klinman, F. S. Mathews
Mutation At A Strictly Conserved, Active Site Tyrosine In The Copper Amine Oxidase Leads To Uncontrolled Oxygenase Activity.
Biochemistry V. 49 7393 2010
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(5, 42)
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: HYDROXY-L-METHIONINE (ME0a)
2b: HYDROXY-L-METHIONINE (ME0b)
2c: HYDROXY-L-METHIONINE (ME0c)
2d: HYDROXY-L-METHIONINE (ME0d)
2e: HYDROXY-L-METHIONINE (ME0e)
2f: HYDROXY-L-METHIONINE (ME0f)
3a: PHOSPHATE ION (PO4a)
3b: PHOSPHATE ION (PO4b)
3c: PHOSPHATE ION (PO4c)
3d: PHOSPHATE ION (PO4d)
3e: PHOSPHATE ION (PO4e)
3f: PHOSPHATE ION (PO4f)
3g: PHOSPHATE ION (PO4g)
3h: PHOSPHATE ION (PO4h)
3i: PHOSPHATE ION (PO4i)
3j: PHOSPHATE ION (PO4j)
3k: PHOSPHATE ION (PO4k)
3l: PHOSPHATE ION (PO4l)
3m: PHOSPHATE ION (PO4m)
3n: PHOSPHATE ION (PO4n)
3o: PHOSPHATE ION (PO4o)
3p: PHOSPHATE ION (PO4p)
3q: PHOSPHATE ION (PO4q)
3r: PHOSPHATE ION (PO4r)
4a: 2,4-BIS(HYDROPEROXY)-5-HYDROXY-L-P... (TY8a)
4b: 2,4-BIS(HYDROPEROXY)-5-HYDROXY-L-P... (TY8b)
4c: 2,4-BIS(HYDROPEROXY)-5-HYDROXY-L-P... (TY8c)
4d: 2,4-BIS(HYDROPEROXY)-5-HYDROXY-L-P... (TY8d)
4e: 2,4-BIS(HYDROPEROXY)-5-HYDROXY-L-P... (TY8e)
4f: 2,4-BIS(HYDROPEROXY)-5-HYDROXY-L-P... (TY8f)
5a: 3,4-BIS(HYDROPEROXY)-5-HYDROXY-L-P... (TY9a)
5b: 3,4-BIS(HYDROPEROXY)-5-HYDROXY-L-P... (TY9b)
5c: 3,4-BIS(HYDROPEROXY)-5-HYDROXY-L-P... (TY9c)
5d: 3,4-BIS(HYDROPEROXY)-5-HYDROXY-L-P... (TY9d)
5e: 3,4-BIS(HYDROPEROXY)-5-HYDROXY-L-P... (TY9e)
5f: 3,4-BIS(HYDROPEROXY)-5-HYDROXY-L-P... (TY9f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CU
6
Ligand/Ion
COPPER (II) ION
2
ME0
6
Mod. Amino Acid
HYDROXY-L-METHIONINE
3
PO4
18
Ligand/Ion
PHOSPHATE ION
4
TY8
6
Mod. Amino Acid
2,4-BIS(HYDROPEROXY)-5-HYDROXY-L-PHENYLALANINE
5
TY9
6
Mod. Residue
3,4-BIS(HYDROPEROXY)-5-HYDROXY-L-PHENYLALANINE
[
close Hetero Component info
]
Sites
(24, 24)
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)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TY8 A:405 , HIS A:456 , HIS A:458 , HIS A:624
BINDING SITE FOR RESIDUE CU A 701
02
AC2
SOFTWARE
PRO A:209 , ASN A:210 , ARG A:211 , HOH A:1250 , HOH A:1373
BINDING SITE FOR RESIDUE PO4 A 702
03
AC3
SOFTWARE
HIS A:218 , LYS A:219
BINDING SITE FOR RESIDUE PO4 A 703
04
AC4
SOFTWARE
GLY A:594 , VAL A:595 , ARG A:596 , HOH A:1324 , HOH A:1393
BINDING SITE FOR RESIDUE PO4 A 704
05
AC5
SOFTWARE
TY8 B:405 , HIS B:456 , HIS B:458 , HIS B:624
BINDING SITE FOR RESIDUE CU B 701
06
AC6
SOFTWARE
PRO B:209 , ASN B:210 , ARG B:211 , HOH B:1250 , HOH B:1373
BINDING SITE FOR RESIDUE PO4 B 702
07
AC7
SOFTWARE
HIS B:218 , LYS B:219
BINDING SITE FOR RESIDUE PO4 B 703
08
AC8
SOFTWARE
GLY B:594 , VAL B:595 , ARG B:596 , HOH B:1324 , HOH B:1393
BINDING SITE FOR RESIDUE PO4 B 704
09
AC9
SOFTWARE
TY8 C:405 , HIS C:456 , HIS C:458 , HIS C:624
BINDING SITE FOR RESIDUE CU C 701
10
BC1
SOFTWARE
PRO C:209 , ASN C:210 , ARG C:211 , HOH C:1250 , HOH C:1373
BINDING SITE FOR RESIDUE PO4 C 702
11
BC2
SOFTWARE
HIS C:218 , LYS C:219
BINDING SITE FOR RESIDUE PO4 C 703
12
BC3
SOFTWARE
GLY C:594 , VAL C:595 , ARG C:596 , HOH C:1324 , HOH C:1393
BINDING SITE FOR RESIDUE PO4 C 704
13
BC4
SOFTWARE
TY8 D:405 , HIS D:456 , HIS D:458 , HIS D:624
BINDING SITE FOR RESIDUE CU D 701
14
BC5
SOFTWARE
PRO D:209 , ASN D:210 , ARG D:211 , HOH D:1250 , HOH D:1373
BINDING SITE FOR RESIDUE PO4 D 702
15
BC6
SOFTWARE
HIS D:218 , LYS D:219
BINDING SITE FOR RESIDUE PO4 D 703
16
BC7
SOFTWARE
GLY D:594 , VAL D:595 , ARG D:596 , HOH D:1324 , HOH D:1393
BINDING SITE FOR RESIDUE PO4 D 704
17
BC8
SOFTWARE
TY8 E:405 , HIS E:456 , HIS E:458 , HIS E:624
BINDING SITE FOR RESIDUE CU E 701
18
BC9
SOFTWARE
PRO E:209 , ASN E:210 , ARG E:211 , HOH E:1250 , HOH E:1373
BINDING SITE FOR RESIDUE PO4 E 702
19
CC1
SOFTWARE
HIS E:218 , LYS E:219
BINDING SITE FOR RESIDUE PO4 E 703
20
CC2
SOFTWARE
GLY E:594 , VAL E:595 , ARG E:596 , HOH E:1324 , HOH E:1393
BINDING SITE FOR RESIDUE PO4 E 704
21
CC3
SOFTWARE
TY8 F:405 , HIS F:456 , HIS F:458 , HIS F:624
BINDING SITE FOR RESIDUE CU F 701
22
CC4
SOFTWARE
PRO F:209 , ASN F:210 , ARG F:211 , HOH F:1250 , HOH F:1373
BINDING SITE FOR RESIDUE PO4 F 702
23
CC5
SOFTWARE
HIS F:218 , LYS F:219
BINDING SITE FOR RESIDUE PO4 F 703
24
CC6
SOFTWARE
GLY F:594 , VAL F:595 , ARG F:596 , HOH F:1324 , HOH F:1393
BINDING SITE FOR RESIDUE PO4 F 704
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(2, 12)
Info
All PROSITE Patterns/Profiles
1: COPPER_AMINE_OXID_1 (A:394-407,B:394-407,C:394-407,D:39...)
2: COPPER_AMINE_OXID_2 (A:619-632,B:619-632,C:619-632,D:61...)
;
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
6
A:394-407
B:394-407
C:394-407
D:394-407
E:394-407
F:394-407
2
COPPER_AMINE_OXID_2
PS01165
Copper amine oxidase copper-binding site signature.
AMO_PICAN
619-632
6
A:619-632
B:619-632
C:619-632
D:619-632
E:619-632
F:619-632
[
close PROSITE info
]
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
(0, 0)
Info
All SCOP Domains
View:
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Label:
Sorry, no Info available
[
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CATH Domains
(0, 0)
Info
all CATH domains
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Label:
Sorry, no Info available
[
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Pfam Domains
(3, 18)
Info
all PFAM domains
1a: PFAM_Cu_amine_oxidN2_3nbjF01 (F:23-109)
1b: PFAM_Cu_amine_oxidN2_3nbjF02 (F:23-109)
1c: PFAM_Cu_amine_oxidN2_3nbjF03 (F:23-109)
1d: PFAM_Cu_amine_oxidN2_3nbjF04 (F:23-109)
1e: PFAM_Cu_amine_oxidN2_3nbjF05 (F:23-109)
1f: PFAM_Cu_amine_oxidN2_3nbjF06 (F:23-109)
2a: PFAM_Cu_amine_oxidN3_3nbjF07 (F:114-216)
2b: PFAM_Cu_amine_oxidN3_3nbjF08 (F:114-216)
2c: PFAM_Cu_amine_oxidN3_3nbjF09 (F:114-216)
2d: PFAM_Cu_amine_oxidN3_3nbjF10 (F:114-216)
2e: PFAM_Cu_amine_oxidN3_3nbjF11 (F:114-216)
2f: PFAM_Cu_amine_oxidN3_3nbjF12 (F:114-216)
3a: PFAM_Cu_amine_oxid_3nbjF13 (F:241-662)
3b: PFAM_Cu_amine_oxid_3nbjF14 (F:241-662)
3c: PFAM_Cu_amine_oxid_3nbjF15 (F:241-662)
3d: PFAM_Cu_amine_oxid_3nbjF16 (F:241-662)
3e: PFAM_Cu_amine_oxid_3nbjF17 (F:241-662)
3f: PFAM_Cu_amine_oxid_3nbjF18 (F:241-662)
View:
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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_oxidN2-3nbjF01
F:23-109
1b
Cu_amine_oxidN2-3nbjF02
F:23-109
1c
Cu_amine_oxidN2-3nbjF03
F:23-109
1d
Cu_amine_oxidN2-3nbjF04
F:23-109
1e
Cu_amine_oxidN2-3nbjF05
F:23-109
1f
Cu_amine_oxidN2-3nbjF06
F:23-109
Family
:
Cu_amine_oxidN3
(37)
Pichia angusta (Yeast) (Hansenula polymorpha)
(5)
2a
Cu_amine_oxidN3-3nbjF07
F:114-216
2b
Cu_amine_oxidN3-3nbjF08
F:114-216
2c
Cu_amine_oxidN3-3nbjF09
F:114-216
2d
Cu_amine_oxidN3-3nbjF10
F:114-216
2e
Cu_amine_oxidN3-3nbjF11
F:114-216
2f
Cu_amine_oxidN3-3nbjF12
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-3nbjF13
F:241-662
3b
Cu_amine_oxid-3nbjF14
F:241-662
3c
Cu_amine_oxid-3nbjF15
F:241-662
3d
Cu_amine_oxid-3nbjF16
F:241-662
3e
Cu_amine_oxid-3nbjF17
F:241-662
3f
Cu_amine_oxid-3nbjF18
F:241-662
[
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