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1MYP
Asym. Unit
Info
Asym.Unit (166 KB)
Biol.Unit 1 (159 KB)
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(1)
Title
:
X-RAY CRYSTAL STRUCTURE OF CANINE MYELOPEROXIDASE AT 3 ANGSTROMS RESOLUTION
Authors
:
R. E. Fenna, J. Zeng
Date
:
15 Apr 92 (Deposition) - 31 Jan 94 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Myeloperoxidase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Zeng, R. E. Fenna
X-Ray Crystal Structure Of Canine Myeloperoxidase At 3 A Resolution.
J. Mol. Biol. V. 226 185 1992
[
close entry info
]
Hetero Components
(3, 16)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
2b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
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)
3g: N-ACETYL-D-GLUCOSAMINE (NAGg)
3h: N-ACETYL-D-GLUCOSAMINE (NAGh)
3i: N-ACETYL-D-GLUCOSAMINE (NAGi)
3j: N-ACETYL-D-GLUCOSAMINE (NAGj)
3k: N-ACETYL-D-GLUCOSAMINE (NAGk)
3l: N-ACETYL-D-GLUCOSAMINE (NAGl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
2
Ligand/Ion
CALCIUM ION
2
HEM
2
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
3
NAG
12
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(16, 16)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
NAG A:583 , ASN C:317
BINDING SITE FOR RESIDUE NAG A 582
02
AC2
SOFTWARE
NAG A:582 , LEU B:33 , ARG D:438 , PHE D:439 , CYS D:440 , GLY D:441
BINDING SITE FOR RESIDUE NAG A 583
03
AC3
SOFTWARE
NAG A:585 , ASN C:189 , ASN C:192 , VAL C:199
BINDING SITE FOR RESIDUE NAG A 584
04
AC4
SOFTWARE
NAG A:584
BINDING SITE FOR RESIDUE NAG A 585
05
AC5
SOFTWARE
NAG A:587 , ASN C:225 , ALA C:228 , TRP C:369 , LEU C:373
BINDING SITE FOR RESIDUE NAG A 586
06
AC6
SOFTWARE
NAG A:586
BINDING SITE FOR RESIDUE NAG A 587
07
AC7
SOFTWARE
NAG B:583 , ASN D:317
BINDING SITE FOR RESIDUE NAG B 582
08
AC8
SOFTWARE
LEU A:33 , NAG B:582 , ARG C:438 , PHE C:439 , GLY C:441
BINDING SITE FOR RESIDUE NAG B 583
09
AC9
SOFTWARE
NAG B:585 , ASN D:189 , ASN D:192 , VAL D:199 , GLN D:201
BINDING SITE FOR RESIDUE NAG B 584
10
BC1
SOFTWARE
NAG B:584
BINDING SITE FOR RESIDUE NAG B 585
11
BC2
SOFTWARE
NAG B:587 , ASN D:225 , TRP D:369
BINDING SITE FOR RESIDUE NAG B 586
12
BC3
SOFTWARE
NAG B:586
BINDING SITE FOR RESIDUE NAG B 587
13
BC4
SOFTWARE
ASP A:96 , THR C:168 , PHE C:170 , ASP C:172 , SER C:174
BINDING SITE FOR RESIDUE CA A 581
14
BC5
SOFTWARE
ASP B:96 , THR D:168 , PHE D:170 , ASP D:172 , SER D:174
BINDING SITE FOR RESIDUE CA B 581
15
BC6
SOFTWARE
MET A:87 , GLN A:91 , ASP A:94 , ASP A:98 , PHE A:99 , THR A:100 , ARG C:239 , GLU C:242 , MET C:243 , THR C:329 , PHE C:332 , ARG C:333 , HIS C:336 , ILE C:339 , PHE C:365 , LEU C:406 , PHE C:407 , ARG C:424
BINDING SITE FOR RESIDUE HEM A 580
16
BC7
SOFTWARE
MET B:87 , GLN B:91 , ASP B:94 , ASP B:98 , PHE B:99 , THR B:100 , GLU D:242 , MET D:243 , THR D:329 , PHE D:332 , ARG D:333 , HIS D:336 , ILE D:339 , PHE D:365 , LEU D:406 , PHE D:407 , LEU D:417 , LEU D:420 , ARG D:424
BINDING SITE FOR RESIDUE HEM B 580
[
close Site info
]
SAPs(SNPs)/Variants
(8, 16)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_015377 (Y7C, chain A/B, )
2: VAR_015378 (M85T, chain A/B, )
3: VAR_036517 (R281Q, chain C/D, )
4: VAR_PERM_HUMAN_CCDS11604_1_01 (R281Q, chain C/D, )
5: VAR_015379 (R403W, chain C/D, )
6: VAR_023996 (R438C, chain C/D, )
7: VAR_023997 (E517Q, chain C/D, )
8: VAR_012066 (I551V, chain C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_015377
Y
173
C
PERM_HUMAN
Disease (MPOD)
78950939
A/B
Y
7
C
2
UniProt
VAR_015378
M
251
T
PERM_HUMAN
Disease (MPOD)
56378716
A/B
M
85
T
3
UniProt
VAR_036517
R
447
Q
PERM_HUMAN
Unclassified
---
C/D
R
281
Q
4
CancerSNP
VAR_PERM_HUMAN_CCDS11604_1_01
*
R
447
Q
PERM_HUMAN
Disease (Colorectal cancer)
---
C/D
R
281
Q
5
UniProt
VAR_015379
R
569
W
PERM_HUMAN
Disease (MPOD)
---
C/D
R
403
W
6
UniProt
VAR_023996
R
604
C
PERM_HUMAN
Polymorphism
35670089
C/D
R
438
C
7
UniProt
VAR_023997
E
683
Q
PERM_HUMAN
Polymorphism
35702888
C/D
E
517
Q
8
UniProt
VAR_012066
I
717
V
PERM_HUMAN
Polymorphism
2759
C/D
I
551
V
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: PEROXIDASE_1 (C:242-252,D:242-252)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PEROXIDASE_1
PS00435
Peroxidases proximal heme-ligand signature.
PERM_HUMAN
408-418
2
C:242-252
D:242-252
[
close PROSITE info
]
Exons
(9, 20)
Info
All Exons
Exon 1.4a (A:1-17 | B:1-17 | - | -)
Exon 1.4c (A:17-60 | B:17-60 | - | -)
Exon 1.5 (A:61-104 | B:61-104 | C:114-129 | ...)
Exon 1.6 (- | - | C:130-236 | D:130-236)
Exon 1.7 (- | - | C:236-289 | D:236-289)
Exon 1.9 (- | - | C:290-375 | D:290-375)
Exon 1.10 (- | - | C:375-432 | D:375-432)
Exon 1.11 (- | - | C:432-511 | D:432-511)
Exon 1.12 (- | - | C:511-575 | D:511-575)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.3/1.4a
02: Boundary 1.4a/1.4c
03: Boundary 1.4c/1.5
04: Boundary 1.5/1.6
05: Boundary 1.6/1.7
06: Boundary 1.7/1.9
07: Boundary 1.9/1.10
08: Boundary 1.10/1.11
09: Boundary 1.11/1.12
10: Boundary 1.12/-
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
1.1
ENST00000225275
1
ENSE00001151667
chr17:
56358296-56357966
331
PERM_HUMAN
1-52
52
0
-
-
1.2
ENST00000225275
2
ENSE00000739393
chr17:
56357820-56357727
94
PERM_HUMAN
52-83
32
0
-
-
1.3
ENST00000225275
3
ENSE00000739378
chr17:
56357375-56357200
176
PERM_HUMAN
83-142
60
0
-
-
1.4a
ENST00000225275
4a
ENSE00000739375
chr17:
56357007-56356884
124
PERM_HUMAN
142-183
42
2
A:1-17
B:1-17
-
-
17
17
-
-
1.4c
ENST00000225275
4c
ENSE00000739356
chr17:
56356787-56356658
130
PERM_HUMAN
183-226
44
2
A:17-60
B:17-60
-
-
44
44
-
-
1.5
ENST00000225275
5
ENSE00000480273
chr17:
56356575-56356369
207
PERM_HUMAN
227-295
69
4
A:61-104
B:61-104
C:114-129
D:114-129
44
44
16
16
1.6
ENST00000225275
6
ENSE00000480274
chr17:
56355506-56355188
319
PERM_HUMAN
296-402
107
2
-
-
C:130-236
D:130-236
-
-
107
107
1.7
ENST00000225275
7
ENSE00000739352
chr17:
56353063-56352903
161
PERM_HUMAN
402-455
54
2
-
-
C:236-289
D:236-289
-
-
54
54
1.9
ENST00000225275
9
ENSE00000480276
chr17:
56351030-56350775
256
PERM_HUMAN
456-541
86
2
-
-
C:290-375
D:290-375
-
-
86
86
1.10
ENST00000225275
10
ENSE00001743415
chr17:
56350279-56350109
171
PERM_HUMAN
541-598
58
2
-
-
C:375-432
D:375-432
-
-
58
58
1.11
ENST00000225275
11
ENSE00000739347
chr17:
56349253-56349016
238
PERM_HUMAN
598-677
80
2
-
-
C:432-511
D:432-511
-
-
80
80
1.12
ENST00000225275
12
ENSE00001151664
chr17:
56348224-56347217
1008
PERM_HUMAN
677-745
69
2
-
-
C:511-575
D:511-575
-
-
65
65
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1myp_1 (A:,C:)
1b: SCOP_d1myp_2 (B:,D:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Heme-dependent peroxidases
(402)
Superfamily
:
Heme-dependent peroxidases
(402)
Family
:
Myeloperoxidase-like
(44)
Protein domain
:
Myeloperoxidase
(8)
Dog (Canis familiaris) [TaxId: 9615]
(1)
1a
d1myp.1
A:,C:
1b
d1myp.2
B:,D:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1mypC00 (C:114-575)
1b: CATH_1mypD00 (D:114-575)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Myeloperoxidase, subunit C
(39)
Homologous Superfamily
:
Myeloperoxidase, subunit C
(39)
Dog (Canis lupus familiaris)
(1)
1a
1mypC00
C:114-575
1b
1mypD00
D:114-575
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_An_peroxidase_1mypD01 (D:114-552)
1b: PFAM_An_peroxidase_1mypD02 (D:114-552)
1c: PFAM_An_peroxidase_1mypD03 (D:114-552)
1d: PFAM_An_peroxidase_1mypD04 (D:114-552)
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Clans
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)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: An_peroxidase]
(45)
Family
:
An_peroxidase
(45)
Homo sapiens (Human)
(2)
1a
An_peroxidase-1mypD01
D:114-552
1b
An_peroxidase-1mypD02
D:114-552
1c
An_peroxidase-1mypD03
D:114-552
1d
An_peroxidase-1mypD04
D:114-552
[
close Pfam info
]
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