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3F9P
Asym. Unit
Info
Asym.Unit (191 KB)
Biol.Unit 1 (94 KB)
Biol.Unit 2 (94 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF MYELOPEROXIDASE FROM HUMAN LEUKOCYTES
Authors
:
X. Carpena, I. Fita, C. Obinger
Date
:
14 Nov 08 (Deposition) - 14 Jul 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.93
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,C (1x)
Biol. Unit 2: B,D (1x)
Keywords
:
Imidazolate, Myeloperoxidase, Heme To Protein Linkage, Peroxidase- Cyclooxygenase Superfamily, Disease Mutation, Glycoprotein, Hydrogen Peroxide, Iron, Lysosome, Metal-Binding, Oxidation, Oxidoreductase, Disulfide Bond, Heme, Peroxidase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
X. Carpena, P. Vidossich, K. Schroettner, B. M. Calisto, S. Banerjee, J. Stampler, M. Soudi, P. G. Furtmuller, C. Rovira, I. Fita, C. Obinger
Essential Role Of Proximal Histidine-Asparagine Interaction In Mammalian Peroxidases.
J. Biol. Chem. V. 284 25929 2009
[
close entry info
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Hetero Components
(8, 26)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
2a: BETA-D-MANNOSE (BMAa)
2b: BETA-D-MANNOSE (BMAb)
2c: BETA-D-MANNOSE (BMAc)
2d: BETA-D-MANNOSE (BMAd)
2e: BETA-D-MANNOSE (BMAe)
2f: BETA-D-MANNOSE (BMAf)
3a: CALCIUM ION (CAa)
3b: CALCIUM ION (CAb)
4a: CHLORIDE ION (CLa)
4b: CHLORIDE ION (CLb)
5a: S-HYDROXYCYSTEINE (CSOa)
5b: S-HYDROXYCYSTEINE (CSOb)
6a: ALPHA-L-FUCOSE (FUCa)
6b: ALPHA-L-FUCOSE (FUCb)
7a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
7b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
8a: N-ACETYL-D-GLUCOSAMINE (NAGa)
8b: N-ACETYL-D-GLUCOSAMINE (NAGb)
8c: N-ACETYL-D-GLUCOSAMINE (NAGc)
8d: N-ACETYL-D-GLUCOSAMINE (NAGd)
8e: N-ACETYL-D-GLUCOSAMINE (NAGe)
8f: N-ACETYL-D-GLUCOSAMINE (NAGf)
8g: N-ACETYL-D-GLUCOSAMINE (NAGg)
8h: N-ACETYL-D-GLUCOSAMINE (NAGh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
2
Ligand/Ion
ACETATE ION
2
BMA
6
Ligand/Ion
BETA-D-MANNOSE
3
CA
2
Ligand/Ion
CALCIUM ION
4
CL
2
Ligand/Ion
CHLORIDE ION
5
CSO
2
Mod. Amino Acid
S-HYDROXYCYSTEINE
6
FUC
2
Ligand/Ion
ALPHA-L-FUCOSE
7
HEM
2
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
8
NAG
8
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
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
ASP A:96 , THR C:168 , PHE C:170 , ASP C:172 , SER C:174
BINDING SITE FOR RESIDUE CA C 601
02
AC2
SOFTWARE
ARG A:31 , TRP A:32 , ASN C:326 , VAL C:327 , TRP C:436
BINDING SITE FOR RESIDUE CL A 602
03
AC3
SOFTWARE
MET A:87 , GLY A:90 , 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 , GLY C:335 , HIS C:336 , ILE C:339 , PHE C:365 , PHE C:407 , LEU C:417 , LEU C:420 , ARG C:424
BINDING SITE FOR RESIDUE HEM A 605
04
AC4
SOFTWARE
ASN C:189 , ASN C:192 , ALA C:198 , VAL C:199 , GLN C:201
BINDING SITE FOR RESIDUE NAG C 620
05
AC5
SOFTWARE
ASN C:225 , TRP C:369
BINDING SITE FOR RESIDUE NAG C 630
06
AC6
SOFTWARE
ASN C:317 , VAL C:320 , NAG C:641 , FUC C:645
BINDING SITE FOR RESIDUE NAG C 640
07
AC7
SOFTWARE
NAG C:640 , BMA C:642 , FUC C:645 , PHE D:439 , GLY D:441
BINDING SITE FOR RESIDUE NAG C 641
08
AC8
SOFTWARE
NAG C:641 , BMA C:643 , BMA C:644 , PHE D:439
BINDING SITE FOR RESIDUE BMA C 642
09
AC9
SOFTWARE
BMA C:642 , LYS D:308
BINDING SITE FOR RESIDUE MAN C 643
10
BC1
SOFTWARE
TRP B:32 , BMA C:642 , PHE D:439 , LYS D:505 , FUC D:645
BINDING SITE FOR RESIDUE MAN C 644
11
BC2
SOFTWARE
ARG C:504 , NAG C:640 , NAG C:641 , BMA D:644
BINDING SITE FOR RESIDUE FUC C 645
12
BC3
SOFTWARE
PRO C:124 , ARG C:161
BINDING SITE FOR RESIDUE ACT C 703
13
BC4
SOFTWARE
ASP B:96 , THR D:168 , PHE D:170 , ASP D:172 , SER D:174
BINDING SITE FOR RESIDUE CA D 601
14
BC5
SOFTWARE
TRP B:32 , ASN D:326 , VAL D:327 , TRP D:436
BINDING SITE FOR RESIDUE CL D 602
15
BC6
SOFTWARE
MET B:87 , GLY B:90 , GLN B:91 , ASP B:94 , ASP B:98 , PHE B:99 , THR B:100 , ARG D:239 , GLU D:242 , MET D:243 , THR D:329 , PHE D:332 , ARG D:333 , GLY D:335 , HIS D:336 , PHE D:365 , PHE D:407 , LEU D:417 , ARG D:424
BINDING SITE FOR RESIDUE HEM B 605
16
BC7
SOFTWARE
ASN D:189 , ASN D:192 , ALA D:198 , VAL D:199 , GLN D:201
BINDING SITE FOR RESIDUE NAG D 620
17
BC8
SOFTWARE
ASN D:225 , TRP D:369
BINDING SITE FOR RESIDUE NAG D 630
18
BC9
SOFTWARE
ASN D:317 , VAL D:320 , NAG D:641 , FUC D:645
BINDING SITE FOR RESIDUE NAG D 640
19
CC1
SOFTWARE
PHE C:439 , GLY C:441 , SER D:319 , NAG D:640 , BMA D:642
BINDING SITE FOR RESIDUE NAG D 641
20
CC2
SOFTWARE
PHE C:439 , NAG D:641 , BMA D:643 , BMA D:644
BINDING SITE FOR RESIDUE BMA D 642
21
CC3
SOFTWARE
LYS C:308 , BMA D:642
BINDING SITE FOR RESIDUE MAN D 643
22
CC4
SOFTWARE
PHE C:439 , LYS C:505 , FUC C:645 , BMA D:642
BINDING SITE FOR RESIDUE MAN D 644
23
CC5
SOFTWARE
BMA C:644 , ARG D:504 , NAG D:640
BINDING SITE FOR RESIDUE FUC D 645
24
CC6
SOFTWARE
PRO D:124 , ARG D:161
BINDING SITE FOR RESIDUE ACT D 703
[
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:0-17 | B:0-17 | - | -)
Exon 1.4c (A:17-60 | B:17-60 | - | -)
Exon 1.5 (A:61-106 | B:61-107 | C:113-129 | ...)
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:511-579 | D:511-579)
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:0-17
B:0-17
-
-
18
18
-
-
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:61-106
B:61-107
C:113-129
D:113-129
46
47
17
17
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:511-579
D:511-579
-
-
69
69
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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]
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Chain D
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