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Getting 'Exon' information from database.
2J5W
Asym. Unit
Info
Asym.Unit (184 KB)
Biol.Unit 1 (177 KB)
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(1)
Title
:
CERULOPLASMIN REVISITED: STRUCTURAL AND FUNCTIONAL ROLES OF VARIOUS METAL CATION BINDING SITES
Authors
:
I. Bento, C. Peixoto, V. N. Zaitsev, P. F. Lindley
Date
:
19 Sep 06 (Deposition) - 06 Feb 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Oxidoreductase, Plasma Protein, Copper Transport, Copper, Transport, Polymorphism, Glycoprotein, Multi-Copper Oxidase, Ceruloplasmin, Metal-Binding, Ion Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
I. Bento, C. Peixoto, V. N. Zaitsev, P. F. Lindley
Ceruloplasmin Revisited: Structural And Functional Roles Of Various Metal Cation-Binding Sites.
Acta Crystallogr. , Sect. D V. 63 240 2007
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Hetero Components
(7, 17)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
2a: COPPER (II) ION (CUa)
2b: COPPER (II) ION (CUb)
2c: COPPER (II) ION (CUc)
2d: COPPER (II) ION (CUd)
2e: COPPER (II) ION (CUe)
2f: COPPER (II) ION (CUf)
2g: COPPER (II) ION (CUg)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
5a: N-ACETYL-D-GLUCOSAMINE (NAGa)
5b: N-ACETYL-D-GLUCOSAMINE (NAGb)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
4c: SODIUM ION (NAc)
7a: OXYGEN MOLECULE (OXYa)
6a: OXYGEN ATOM (Oa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
1
Ligand/Ion
CALCIUM ION
2
CU
7
Ligand/Ion
COPPER (II) ION
3
GOL
2
Ligand/Ion
GLYCEROL
4
NA
3
Ligand/Ion
SODIUM ION
5
NAG
2
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
6
O
1
Ligand/Ion
OXYGEN ATOM
7
OXY
1
Ligand/Ion
OXYGEN MOLECULE
[
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Sites
(17, 17)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:119 , ILE A:1016 , HOH A:2339 , HOH A:2340
BINDING SITE FOR RESIDUE NAG A3055
02
AC2
SOFTWARE
ASN A:378
BINDING SITE FOR RESIDUE NAG A3056
03
AC3
SOFTWARE
LYS A:109 , GLN A:124 , ASP A:127 , ASP A:128 , HOH A:2025 , HOH A:2030
BINDING SITE FOR RESIDUE CA A3042
04
AC4
SOFTWARE
TYR A:36 , GLY A:45 , TYR A:48 , SER A:237
BINDING SITE FOR RESIDUE NA A3043
05
AC5
SOFTWARE
PHE A:389 , GLY A:398 , TYR A:401 , SER A:598 , MET A:601 , HOH A:2101
BINDING SITE FOR RESIDUE NA A3044
06
AC6
SOFTWARE
PHE A:748 , GLY A:757 , TYR A:760 , SER A:936 , MET A:939 , HOH A:2217
BINDING SITE FOR RESIDUE NA A3045
07
AC7
SOFTWARE
HIS A:276 , CYS A:319 , HIS A:324 , LEU A:329
BINDING SITE FOR RESIDUE CU A3046
08
AC8
SOFTWARE
HIS A:163 , HIS A:980 , HIS A:1020 , HOH A:2338 , OXY A:3054
BINDING SITE FOR RESIDUE CU A3047
09
AC9
SOFTWARE
HIS A:103 , HIS A:161 , HIS A:1022 , OXY A:3054
BINDING SITE FOR RESIDUE CU A3048
10
BC1
SOFTWARE
HIS A:101 , HIS A:103 , HIS A:978 , HIS A:980 , HOH A:2337 , O A:3050 , OXY A:3054
BINDING SITE FOR RESIDUE CU A3049
11
BC2
SOFTWARE
HIS A:637 , CYS A:680 , HIS A:685 , MET A:690
BINDING SITE FOR RESIDUE CU A3051
12
BC3
SOFTWARE
LEU A:974 , HIS A:975 , CYS A:1021 , HIS A:1026 , MET A:1031
BINDING SITE FOR RESIDUE CU A3052
13
BC4
SOFTWARE
GLU A:272 , HIS A:940 , ASP A:1025 , HOH A:2295 , HOH A:2296 , HOH A:2327
BINDING SITE FOR RESIDUE CU A3053
14
BC5
SOFTWARE
HIS A:101 , SER A:102 , TYR A:107 , HIS A:978 , HOH A:2337 , CU A:3049
BINDING SITE FOR RESIDUE O A3050
15
BC6
SOFTWARE
HIS A:101 , HIS A:103 , HIS A:161 , HIS A:163 , HIS A:978 , HIS A:980 , HIS A:1022 , HOH A:2338 , CU A:3047 , CU A:3048 , CU A:3049
BINDING SITE FOR RESIDUE OXY A3054
16
BC7
SOFTWARE
TYR A:646 , TRP A:648 , ARG A:653 , ASN A:657 , HOH A:2168
BINDING SITE FOR RESIDUE GOL A3057
17
BC8
SOFTWARE
PRO A:167 , ILE A:170 , VAL A:204 , VAL A:205 , ASP A:206 , THR A:1024 , HOH A:2050 , HOH A:2341
BINDING SITE FOR RESIDUE GOL A3058
[
close Site info
]
SAPs(SNPs)/Variants
(7, 7)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_025655 (I44T, chain A, )
2: VAR_032815 (R348C, chain A, )
3: VAR_025656 (P458L, chain A, )
4: VAR_025657 (D525E, chain A, )
5: VAR_025658 (T532I, chain A, )
6: VAR_025659 (R774H, chain A, )
7: VAR_025660 (T822R, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_025655
I
63
T
CERU_HUMAN
Unclassified
---
A
I
44
T
2
UniProt
VAR_032815
R
367
C
CERU_HUMAN
Polymorphism
34624984
A
R
348
C
3
UniProt
VAR_025656
P
477
L
CERU_HUMAN
Polymorphism
35331711
A
P
458
L
4
UniProt
VAR_025657
D
544
E
CERU_HUMAN
Polymorphism
701753
A
D
525
E
5
UniProt
VAR_025658
T
551
I
CERU_HUMAN
Polymorphism
---
A
T
532
I
6
UniProt
VAR_025659
R
793
H
CERU_HUMAN
Polymorphism
---
A
R
774
H
7
UniProt
VAR_025660
T
841
R
CERU_HUMAN
Polymorphism
56033670
A
T
822
R
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: MULTICOPPER_OXIDASE1 (A:313-333|A:674-694|A:1015-1035)
2: MULTICOPPER_OXIDASE2 (A:1020-1031)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
MULTICOPPER_OXIDASE1
PS00079
Multicopper oxidases signature 1.
CERU_HUMAN
332-352
693-713
1034-1054
3
A:313-333
A:674-694
A:1015-1035
2
MULTICOPPER_OXIDASE2
PS00080
Multicopper oxidases signature 2.
CERU_HUMAN
1039-1050
1
A:1020-1031
[
close PROSITE info
]
Exons
(18, 18)
Info
All Exons
Exon 1.1a (A:1-30)
Exon 1.3 (A:30-113)
Exon 1.4b (A:113-184)
Exon 1.5a (A:184-242)
Exon 1.6b (A:242-327)
Exon 1.7 (A:327-384)
Exon 1.8 (A:384-431)
Exon 1.9b (A:431-475)
Exon 1.10a (A:483-552)
Exon 1.11b (A:553-603)
Exon 1.12a (A:603-674)
Exon 1.13a (A:674-743)
Exon 1.14 (A:743-790)
Exon 1.15 (A:790-833)
Exon 1.16c (A:833-868)
Exon 1.17 (A:869-941 (gaps))
Exon 1.18a (A:941-987)
Exon 1.19c (A:988-1041)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1a
02: Boundary 1.1a/1.3
03: Boundary 1.3/1.4b
04: Boundary 1.4b/1.5a
05: Boundary 1.5a/1.6b
06: Boundary 1.6b/1.7
07: Boundary 1.7/1.8
08: Boundary 1.8/1.9b
09: Boundary 1.9b/1.10a
10: Boundary 1.10a/1.11b
11: Boundary 1.11b/1.12a
12: Boundary 1.12a/1.13a
13: Boundary 1.13a/1.14
14: Boundary 1.14/1.15
15: Boundary 1.15/1.16c
16: Boundary 1.16c/1.17
17: Boundary 1.17/1.18a
18: Boundary 1.18a/1.19c
19: Boundary 1.19c/1.20c
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1a
ENST00000264613
1a
ENSE00001008197
chr3:
148939842-148939434
409
CERU_HUMAN
1-49
49
1
A:1-30
30
1.3
ENST00000264613
3
ENSE00001893178
chr3:
148930485-148930238
248
CERU_HUMAN
49-132
84
1
A:30-113
84
1.4b
ENST00000264613
4b
ENSE00001245608
chr3:
148928166-148927954
213
CERU_HUMAN
132-203
72
1
A:113-184
72
1.5a
ENST00000264613
5a
ENSE00001245605
chr3:
148927171-148926998
174
CERU_HUMAN
203-261
59
1
A:184-242
59
1.6b
ENST00000264613
6b
ENSE00001008187
chr3:
148925404-148925150
255
CERU_HUMAN
261-346
86
1
A:242-327
86
1.7
ENST00000264613
7
ENSE00001008205
chr3:
148924126-148923955
172
CERU_HUMAN
346-403
58
1
A:327-384
58
1.8
ENST00000264613
8
ENSE00001008195
chr3:
148920028-148919889
140
CERU_HUMAN
403-450
48
1
A:384-431
48
1.9b
ENST00000264613
9b
ENSE00001008184
chr3:
148917651-148917499
153
CERU_HUMAN
450-501
52
1
A:431-475
45
1.10a
ENST00000264613
10a
ENSE00001008182
chr3:
148916365-148916154
212
CERU_HUMAN
501-571
71
1
A:483-552
70
1.11b
ENST00000264613
11b
ENSE00001008188
chr3:
148905989-148905839
151
CERU_HUMAN
572-622
51
1
A:553-603
51
1.12a
ENST00000264613
12a
ENSE00001008204
chr3:
148904519-148904307
213
CERU_HUMAN
622-693
72
1
A:603-674
72
1.13a
ENST00000264613
13a
ENSE00001008200
chr3:
148903233-148903026
208
CERU_HUMAN
693-762
70
1
A:674-743
70
1.14
ENST00000264613
14
ENSE00001008190
chr3:
148901392-148901253
140
CERU_HUMAN
762-809
48
1
A:743-790
48
1.15
ENST00000264613
15
ENSE00001008201
chr3:
148899920-148899792
129
CERU_HUMAN
809-852
44
1
A:790-833
44
1.16c
ENST00000264613
16c
ENSE00000779559
chr3:
148897449-148897343
107
CERU_HUMAN
852-887
36
1
A:833-868
36
1.17
ENST00000264613
17
ENSE00001245534
chr3:
148896418-148896202
217
CERU_HUMAN
888-960
73
1
A:869-941 (gaps)
73
1.18a
ENST00000264613
18a
ENSE00001245525
chr3:
148895766-148895627
140
CERU_HUMAN
960-1006
47
1
A:941-987
47
1.19c
ENST00000264613
19c
ENSE00001245656
chr3:
148894199-148894037
163
CERU_HUMAN
1007-1061
55
1
A:988-1041
54
1.20c
ENST00000264613
20c
ENSE00001915536
chr3:
148891517-148890286
1232
CERU_HUMAN
1061-1065
5
0
-
-
[
close EXON info
]
SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d2j5wa1 (A:1-192)
1b: SCOP_d2j5wa2 (A:554-705)
1c: SCOP_d2j5wa3 (A:339-553)
1d: SCOP_d2j5wa4 (A:706-884)
1e: SCOP_d2j5wa5 (A:890-1041)
1f: SCOP_d2j5wa6 (A:193-338)
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Protein Domains
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Organisms
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(
)
Class
:
All beta proteins
(24004)
Fold
:
Cupredoxin-like
(545)
Superfamily
:
Cupredoxins
(543)
Family
:
automated matches
(57)
Protein domain
:
automated matches
(57)
Human (Homo sapiens) [TaxId: 9606]
(5)
1a
d2j5wa1
A:1-192
1b
d2j5wa2
A:554-705
1c
d2j5wa3
A:339-553
1d
d2j5wa4
A:706-884
1e
d2j5wa5
A:890-1041
1f
d2j5wa6
A:193-338
[
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CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_2j5wA02 (A:193-342)
1b: CATH_2j5wA06 (A:891-1041)
1c: CATH_2j5wA04 (A:554-705)
1d: CATH_2j5wA05 (A:706-890)
1e: CATH_2j5wA01 (A:1-192)
1f: CATH_2j5wA03 (A:343-553)
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Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Cupredoxins - blue copper proteins
(420)
Human (Homo sapiens)
(5)
1a
2j5wA02
A:193-342
1b
2j5wA06
A:891-1041
1c
2j5wA04
A:554-705
1d
2j5wA05
A:706-890
1e
2j5wA01
A:1-192
1f
2j5wA03
A:343-553
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
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