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1W7C
Asym. Unit
Info
Asym.Unit (416 KB)
Biol.Unit 1 (809 KB)
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(1)
Title
:
PPLO AT 1.23 ANGSTROMS
Authors
:
A. P. Duff, A. E. Cohen, P. J. Ellis, J. M. Guss
Date
:
01 Sep 04 (Deposition) - 31 Aug 06 (Release) - 16 Jan 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.23
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Amine Oxidase, Oxidoreductase, Quinoprotein, Topaquinone Enzyme
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. P. Duff, A. E. Cohen, P. J. Ellis, K. Hilmer, D. B. Langley, D. M. Dooley, H. C. Freeman, J. M. Guss
The 1. 23 A Structure Of Pichia Pastoris Lysyl Oxidase Reveals A Lysine-Lysine Cross-Link
Acta Crystallogr. , Sect. D V. 62 1073 2006
[
close entry info
]
Hetero Components
(8, 22)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
3a: CHLORIDE ION (CLa)
3b: CHLORIDE ION (CLb)
3c: CHLORIDE ION (CLc)
3d: CHLORIDE ION (CLd)
3e: CHLORIDE ION (CLe)
4a: COPPER (II) ION (CUa)
5a: IMIDAZOLE (IMDa)
6a: MAGNESIUM ION (MGa)
6b: MAGNESIUM ION (MGb)
6c: MAGNESIUM ION (MGc)
6d: MAGNESIUM ION (MGd)
6e: MAGNESIUM ION (MGe)
7a: N-ACETYL-D-GLUCOSAMINE (NAGa)
7b: N-ACETYL-D-GLUCOSAMINE (NAGb)
7c: N-ACETYL-D-GLUCOSAMINE (NAGc)
7d: N-ACETYL-D-GLUCOSAMINE (NAGd)
7e: N-ACETYL-D-GLUCOSAMINE (NAGe)
7f: N-ACETYL-D-GLUCOSAMINE (NAGf)
8a: 5-(2-CARBOXY-2-AMINOETHYL)-2-HYDRO... (TPQa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
1
Ligand/Ion
BETA-D-MANNOSE
2
CA
2
Ligand/Ion
CALCIUM ION
3
CL
5
Ligand/Ion
CHLORIDE ION
4
CU
1
Ligand/Ion
COPPER (II) ION
5
IMD
1
Ligand/Ion
IMIDAZOLE
6
MG
5
Ligand/Ion
MAGNESIUM ION
7
NAG
6
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
8
TPQ
1
Mod. Amino Acid
5-(2-CARBOXY-2-AMINOETHYL)-2-HYDROXY-1,4-BENZOQUINONE
[
close Hetero Component info
]
Sites
(19, 19)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:528 , HIS A:530 , HIS A:694 , HOH A:3035
BINDING SITE FOR RESIDUE CU A 801
02
AC2
SOFTWARE
ASP A:537 , LEU A:538 , ASP A:539 , ASP A:683 , ILE A:684 , HOH A:2742
BINDING SITE FOR RESIDUE CA A 802
03
AC3
SOFTWARE
GLU A:580 , PHE A:673 , ASP A:675 , GLU A:677 , HOH A:2903 , HOH A:2904
BINDING SITE FOR RESIDUE CA A 803
04
AC4
SOFTWARE
HOH A:2052 , HOH A:2054 , HOH A:2059 , HOH A:2060 , HOH A:2645 , HOH A:2649
BINDING SITE FOR RESIDUE MG A 804
05
AC5
SOFTWARE
HOH A:2097 , HOH A:2190 , HOH A:2191 , HOH A:2400 , HOH A:2795 , HOH A:2803
BINDING SITE FOR RESIDUE MG A 805
06
AC6
SOFTWARE
HOH A:2024 , HOH A:2252 , HOH A:2551 , HOH A:2552 , HOH A:2556 , HOH A:2561
BINDING SITE FOR RESIDUE MG A 806
07
AC7
SOFTWARE
HOH A:2100 , HOH A:2243 , HOH A:2248 , HOH A:2792 , HOH A:2793
BINDING SITE FOR RESIDUE MG A 807
08
AC8
SOFTWARE
HOH A:2021 , HOH A:2022 , HOH A:2888 , HOH A:2889 , HOH A:2890
BINDING SITE FOR RESIDUE MG A 808
09
AC9
SOFTWARE
LEU A:663 , TYR A:664 , ASP A:665
BINDING SITE FOR RESIDUE CL A 811
10
BC1
SOFTWARE
LYS A:164 , SER A:165 , LYS A:166 , HOH A:2126 , HOH A:2278
BINDING SITE FOR RESIDUE CL A 812
11
BC2
SOFTWARE
ASP A:297 , HOH A:2501 , HOH A:2720 , HOH A:2726
BINDING SITE FOR RESIDUE CL A 813
12
BC3
SOFTWARE
ALA A:573 , ARG A:574 , HOH A:2712 , HOH A:2713
BINDING SITE FOR RESIDUE CL A 814
13
BC4
SOFTWARE
GLY A:420 , TYR A:421 , HOH A:3023
BINDING SITE FOR RESIDUE CL A 815
14
BC5
SOFTWARE
TYR A:396 , ASP A:398 , ILE A:475 , ASN A:477
BINDING SITE FOR RESIDUE IMD A 821
15
BC6
SOFTWARE
ASN A:81 , ASN A:187 , NAG A:1784 , HOH A:3036 , HOH A:3039 , HOH A:3040
BINDING SITE FOR MONO-SACCHARIDE NAG A1780 BOUND TO ASN A 81
16
BC7
SOFTWARE
ASN A:104 , PHE A:158 , THR A:650 , HOH A:2895 , HOH A:3042 , HOH A:3044
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1781 THROUGH BMA A1783 BOUND TO ASN A 104
17
BC8
SOFTWARE
ASN A:187 , ASN A:191 , ARG A:196 , NAG A:1780 , HOH A:2317 , HOH A:2337 , HOH A:3040
BINDING SITE FOR MONO-SACCHARIDE NAG A1784 BOUND TO ASN A 191
18
BC9
SOFTWARE
ASP A:302 , ASN A:309 , SER A:311
BINDING SITE FOR MONO-SACCHARIDE NAG A1785 BOUND TO ASN A 309
19
CC1
SOFTWARE
THR A:423 , ASN A:434
BINDING SITE FOR MONO-SACCHARIDE NAG A1786 BOUND TO ASN A 434
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
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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
(2, 3)
Info
All SCOP Domains
1a: SCOP_d1w7ca1 (A:316-779)
2a: SCOP_d1w7ca2 (A:43-169)
2b: SCOP_d1w7ca3 (A:170-315)
View:
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Classes
(
)
(
)
Folds
(
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(
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(
)
(
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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
:
Lysyl oxidase PplO, domain 3
(3)
Yeast (Pichia pastoris) [TaxId: 4922]
(3)
1a
d1w7ca1
A:316-779
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
:
Lysyl oxidase PplO, domains 1 and 2
(3)
Yeast (Pichia pastoris) [TaxId: 4922]
(3)
2a
d1w7ca2
A:43-169
2b
d1w7ca3
A:170-315
[
close SCOP info
]
CATH Domains
(2, 3)
Info
all CATH domains
1a: CATH_1w7cA03 (A:175-289)
1b: CATH_1w7cA02 (A:58-174)
2a: CATH_1w7cA01 (A:43-57,A:290-779)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
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 pastoris. Organism_taxid: 4922.
(2)
1a
1w7cA03
A:175-289
1b
1w7cA02
A:58-174
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 pastoris. Organism_taxid: 4922.
(2)
2a
1w7cA01
A:43-57,A:290-779
[
close CATH info
]
Pfam Domains
(3, 3)
Info
all PFAM domains
1a: PFAM_Cu_amine_oxidN2_1w7cA01 (A:62-151)
2a: PFAM_Cu_amine_oxid_1w7cA02 (A:323-734)
3a: PFAM_DUF1965_1w7cA03 (A:239-314)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
CuAO_N2_N3
(40)
Family
:
Cu_amine_oxidN2
(27)
Pichia pastoris (Yeast)
(3)
1a
Cu_amine_oxidN2-1w7cA01
A:62-151
Clan
:
no clan defined [family: Cu_amine_oxid]
(40)
Family
:
Cu_amine_oxid
(40)
Pichia pastoris (Yeast)
(3)
2a
Cu_amine_oxid-1w7cA02
A:323-734
Clan
:
no clan defined [family: DUF1965]
(3)
Family
:
DUF1965
(3)
Pichia pastoris (Yeast)
(3)
3a
DUF1965-1w7cA03
A:239-314
[
close Pfam info
]
Atom Selection
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Chain A
Asymmetric Unit 1
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