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3ZS1
Asym. Unit
Info
Asym.Unit (203 KB)
Biol.Unit 1 (100 KB)
Biol.Unit 2 (100 KB)
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(1)
Title
:
HUMAN MYELOPEROXIDASE INACTIVATED BY TX5
Authors
:
A. K. Tiden, T. Sjogren, M. Svensson, A. Bernlind, R. Senthilmohan, F. A H. Norman, P. O. Markgren, S. Gustavsson, S. Schmidt, S. Lundquist, L. N. J. Magon, G. N. Jameson, H. Eriksson, A. J. Kettle
Date
:
21 Jun 11 (Deposition) - 31 Aug 11 (Release) - 28 Jun 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: B,D (1x)
Biol. Unit 2: A,C (1x)
Keywords
:
Oxidoreductase, Enzyme Inactivation, Inflammation, Neutrophil, Reactive Oxygen Species (Ros), Hypochlorous Acid
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. K. Tiden, T. Sjogren, M. Svensson, A. Bernlind, R. Senthilmohan, F. Auchere, H. Norman, P. O. Markgren, S. Gustavsson, S. Schmidt, S. Lundquist, L. V. Forbes, N. J. Magon, L. N. Paton, G. N. Jameson, H. Eriksson, A. J. Kettle
2-Thioxanthines Are Mechanism-Based Inactivators Of Myeloperoxidase That Block Oxidative Stress During Inflammation.
J. Biol. Chem. V. 286 37578 2011
[
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Hetero Components
(10, 30)
Info
All Hetero Components
01a: ACETATE ION (ACTa)
01b: ACETATE ION (ACTb)
01c: ACETATE ION (ACTc)
01d: ACETATE ION (ACTd)
01e: ACETATE ION (ACTe)
01f: ACETATE ION (ACTf)
02a: BETA-D-MANNOSE (BMAa)
02b: BETA-D-MANNOSE (BMAb)
03a: CALCIUM ION (CAa)
03b: CALCIUM ION (CAb)
04a: CHLORIDE ION (CLa)
04b: CHLORIDE ION (CLb)
05a: S-HYDROXYCYSTEINE (CSOa)
05b: S-HYDROXYCYSTEINE (CSOb)
06a: ALPHA-L-FUCOSE (FUCa)
07a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
07b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
08a: N-ACETYL-D-GLUCOSAMINE (NAGa)
08b: N-ACETYL-D-GLUCOSAMINE (NAGb)
08c: N-ACETYL-D-GLUCOSAMINE (NAGc)
08d: N-ACETYL-D-GLUCOSAMINE (NAGd)
08e: N-ACETYL-D-GLUCOSAMINE (NAGe)
08f: N-ACETYL-D-GLUCOSAMINE (NAGf)
08g: N-ACETYL-D-GLUCOSAMINE (NAGg)
08h: N-ACETYL-D-GLUCOSAMINE (NAGh)
09a: 3-(2-METHOXYETHYL)-2-THIOXO-1,2,3,... (PVWa)
09b: 3-(2-METHOXYETHYL)-2-THIOXO-1,2,3,... (PVWb)
10a: SULFATE ION (SO4a)
10b: SULFATE ION (SO4b)
10c: SULFATE ION (SO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
6
Ligand/Ion
ACETATE ION
2
BMA
2
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
1
Ligand/Ion
ALPHA-L-FUCOSE
7
HEM
2
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
8
NAG
8
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
9
PVW
2
Ligand/Ion
3-(2-METHOXYETHYL)-2-THIOXO-1,2,3,7-TETRAHYDRO-6H-PURIN-6-ONE
10
SO4
3
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(23, 23)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
MET A:87 , GLY A:90 , GLN A:91 , ASP A:94 , ASP A:98 , PHE A:99 , THR A:100 , PVW A:606 , HOH A:2040 , 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 , LEU C:417 , LEU C:420 , ARG C:424
BINDING SITE FOR RESIDUE HEM A 605
02
AC2
SOFTWARE
GLU A:102 , HEM A:605 , HOH A:2041 , ARG C:239 , GLU C:242 , PHE C:407 , HOH C:2043
BINDING SITE FOR RESIDUE PVW A 606
03
AC3
SOFTWARE
MET B:87 , GLY B:90 , GLN B:91 , ASP B:94 , ASP B:98 , PHE B:99 , THR B:100 , PVW B:606 , HOH B:2038 , HOH B:2042 , HOH B:2043 , GLU D:242 , MET D:243 , TYR D:296 , THR D:329 , PHE D:332 , ARG D:333 , GLY D:335 , HIS D:336 , ILE D:339 , PHE D:407 , LEU D:417 , ARG D:424
BINDING SITE FOR RESIDUE HEM B 605
04
AC4
SOFTWARE
HEM B:605 , ARG D:239 , GLU D:242 , PHE D:407
BINDING SITE FOR RESIDUE PVW B 606
05
AC5
SOFTWARE
THR C:304 , LYS C:486 , ARG C:487 , HOH C:2051
BINDING SITE FOR RESIDUE SO4 C 1579
06
AC6
SOFTWARE
ASP A:96 , THR C:168 , PHE C:170 , ASP C:172 , SER C:174
BINDING SITE FOR RESIDUE CA C 1580
07
AC7
SOFTWARE
TRP A:32 , ASN C:326 , VAL C:327 , TRP C:436
BINDING SITE FOR RESIDUE CL C 1581
08
AC8
SOFTWARE
ARG C:229 , THR C:447 , GLY C:449 , GLN C:450
BINDING SITE FOR RESIDUE SO4 C 1582
09
AC9
SOFTWARE
ARG C:525
BINDING SITE FOR RESIDUE ACT C 1583
10
BC1
SOFTWARE
PRO C:124 , ARG C:148 , ARG C:161
BINDING SITE FOR RESIDUE ACT C 1584
11
BC2
SOFTWARE
PRO C:303 , ARG C:307 , ARG C:487
BINDING SITE FOR RESIDUE ACT C 1585
12
BC3
SOFTWARE
THR D:304 , LYS D:486 , ARG D:487
BINDING SITE FOR RESIDUE SO4 D 1579
13
BC4
SOFTWARE
ASP B:96 , THR D:168 , PHE D:170 , ASP D:172 , SER D:174
BINDING SITE FOR RESIDUE CA D 1580
14
BC5
SOFTWARE
ARG B:31 , TRP B:32 , VAL D:327 , TRP D:436
BINDING SITE FOR RESIDUE CL D 1581
15
BC6
SOFTWARE
PRO D:124 , ARG D:148 , ARG D:161
BINDING SITE FOR RESIDUE ACT D 1582
16
BC7
SOFTWARE
MET D:522 , ARG D:525
BINDING SITE FOR RESIDUE ACT D 1583
17
BC8
SOFTWARE
PRO D:303 , ARG D:307 , ARG D:487
BINDING SITE FOR RESIDUE ACT D 1584
18
BC9
SOFTWARE
ASN C:189 , ASN C:192 , ALA C:198 , VAL C:199 , GLN C:201 , HOH C:2023 , HOH C:2094
BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 189 RESIDUES 1620 TO 1620
19
CC1
SOFTWARE
ASN C:225 , HOH C:2037 , HOH C:2095
BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 225 RESIDUES 1630 TO 1630
20
CC2
SOFTWARE
LEU B:33 , ASN C:317 , SER C:319 , VAL C:320 , HOH C:2096 , HOH C:2097 , HOH C:2098 , HOH C:2099 , TYR D:309 , ARG D:438 , PHE D:439 , GLY D:441
BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 317 RESIDUES 1640 TO 1645
21
CC3
SOFTWARE
ASN D:189 , ASN D:192 , ALA D:198 , VAL D:199 , GLN D:201
BINDING SITE FOR CHAIN D OF SUGAR BOUND TO ASN D 189 RESIDUES 2620 TO 2620
22
CC4
SOFTWARE
ASN D:225 , TRP D:369 , LEU D:373
BINDING SITE FOR CHAIN D OF SUGAR BOUND TO ASN D 225 RESIDUES 2630 TO 2630
23
CC5
SOFTWARE
LEU A:33 , TYR C:309 , PHE C:439 , GLY C:441 , HOH C:2075 , ARG D:314 , ASN D:317 , SER D:319 , VAL D:320
BINDING SITE FOR CHAIN D OF SUGAR BOUND TO ASN D 317 RESIDUES 2640 TO 2642
[
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: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:511-578 | D:511-578)
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:113-129
D:113-129
44
44
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:511-578
D:511-578
-
-
68
68
[
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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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