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4C1M
Asym. Unit
Info
Asym.Unit (213 KB)
Biol.Unit 1 (105 KB)
Biol.Unit 2 (105 KB)
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(1)
Title
:
MYELOPEROXIDASE IN COMPLEX WITH THE REVESIBLE INHIBITOR HX1
Authors
:
L. V. Forbes, T. Sjogren, F. Auchere, D. W. Jenkins, B. Thong, D. Laughto P. Hemsley, G. Pairaudeau, H. Eriksson, J. F. Unitt, A. J. Kettle
Date
:
13 Aug 13 (Deposition) - 13 Nov 13 (Release) - 15 Jan 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: B,D (1x)
Biol. Unit 2: A,C (1x)
Keywords
:
Oxidoreductase, Hydroxamate
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. V. Forbes, T. Sjogren, F. Auchere, D. W. Jenkins, B. Thong, D. Laughton, P. Hemsley, G. Pairaudeau, R. Turner, H. Eriksson, J. F. Unitt, A. J. Kettle
Potent Reversible Inhibition Of Myeloperoxidase By Aromatic Hydroxamates
J. Biol. Chem. V. 288 36636 2013
[
close entry info
]
Hetero Components
(12, 35)
Info
All Hetero Components
01a: ACETATE ION (ACTa)
01b: ACETATE ION (ACTb)
01c: ACETATE ION (ACTc)
01d: ACETATE ION (ACTd)
01e: ACETATE ION (ACTe)
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)
06b: ALPHA-L-FUCOSE (FUCb)
07a: GLYCEROL (GOLa)
07b: GLYCEROL (GOLb)
08a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
08b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
09a: ALPHA-D-MANNOSE (MANa)
09b: ALPHA-D-MANNOSE (MANb)
09c: ALPHA-D-MANNOSE (MANc)
09d: ALPHA-D-MANNOSE (MANd)
10a: N-ACETYL-D-GLUCOSAMINE (NAGa)
10b: N-ACETYL-D-GLUCOSAMINE (NAGb)
10c: N-ACETYL-D-GLUCOSAMINE (NAGc)
10d: N-ACETYL-D-GLUCOSAMINE (NAGd)
10e: N-ACETYL-D-GLUCOSAMINE (NAGe)
10f: N-ACETYL-D-GLUCOSAMINE (NAGf)
10g: N-ACETYL-D-GLUCOSAMINE (NAGg)
10h: N-ACETYL-D-GLUCOSAMINE (NAGh)
11a: 2-{[3,5-BIS(TRIFLUOROMETHYL)BENZYL... (NIHa)
11b: 2-{[3,5-BIS(TRIFLUOROMETHYL)BENZYL... (NIHb)
12a: SULFATE ION (SO4a)
12b: SULFATE ION (SO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
5
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
2
Ligand/Ion
ALPHA-L-FUCOSE
7
GOL
2
Ligand/Ion
GLYCEROL
8
HEM
2
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
9
MAN
4
Ligand/Ion
ALPHA-D-MANNOSE
10
NAG
8
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
11
NIH
2
Ligand/Ion
2-{[3,5-BIS(TRIFLUOROMETHYL)BENZYL]AMINO}-N-HYDROXY-6-OXO-1,6-DIHYDROPYRIMIDINE-5-CARBOXAMIDE
12
SO4
2
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(25, 25)
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)
25: CC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
MET A:87 , GLN A:91 , ASP A:94 , ASP A:98 , PHE A:99 , THR A:100 , NIH A:606 , HOH A:2101 , HOH A:2102 , 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 , ARG C:424
BINDING SITE FOR RESIDUE HEM A 605
02
AC2
SOFTWARE
GLN A:91 , HIS A:95 , HEM A:605 , HOH A:2101 , PRO C:220 , THR C:238 , ARG C:239 , GLU C:242 , PHE C:366 , HOH C:2009 , HOH C:2018
BINDING SITE FOR RESIDUE NIH A 606
03
AC3
SOFTWARE
MET B:87 , ASP B:94 , ASP B:98 , PHE B:99 , THR B:100 , NIH B:606 , HOH B:2103 , HOH B:2107 , ARG D:239 , GLU D:242 , MET D:243 , THR D:329 , PHE D:332 , ARG D:333 , GLY D:335 , HIS D:336 , ILE D:339 , PHE D:365 , PHE D:407 , LEU D:417 , ARG D:424
BINDING SITE FOR RESIDUE HEM B 605
04
AC4
SOFTWARE
GLN B:91 , HIS B:95 , HEM B:605 , HOH B:2103 , HOH B:2107 , PRO D:220 , THR D:238 , ARG D:239 , GLU D:242 , PHE D:366 , VAL D:410 , MET D:411
BINDING SITE FOR RESIDUE NIH B 606
05
AC5
SOFTWARE
HOH B:2108
BINDING SITE FOR RESIDUE SO4 B1003
06
AC6
SOFTWARE
THR C:304 , LYS C:486 , ARG C:487 , HOH C:2208
BINDING SITE FOR RESIDUE GOL C 631
07
AC7
SOFTWARE
ASP A:96 , THR C:168 , PHE C:170 , ASP C:172 , SER C:174
BINDING SITE FOR RESIDUE CA C1579
08
AC8
SOFTWARE
TRP A:32 , VAL C:327 , TRP C:436
BINDING SITE FOR RESIDUE CL C1580
09
AC9
SOFTWARE
ARG C:229 , THR C:447 , GLY C:449 , GLN C:450 , HOH C:2193
BINDING SITE FOR RESIDUE SO4 C1581
10
BC1
SOFTWARE
MET C:522 , ARG C:525 , HOH C:2242
BINDING SITE FOR RESIDUE ACT C1582
11
BC2
SOFTWARE
PRO C:303 , ARG C:307 , ARG C:487 , LYS C:488
BINDING SITE FOR RESIDUE ACT C1583
12
BC3
SOFTWARE
THR D:304 , LYS D:486 , ARG D:487
BINDING SITE FOR RESIDUE GOL D 631
13
BC4
SOFTWARE
ASP B:96 , THR D:168 , PHE D:170 , ASP D:172 , SER D:174
BINDING SITE FOR RESIDUE CA D1579
14
BC5
SOFTWARE
ARG B:31 , TRP B:32 , ASN D:326 , VAL D:327 , TRP D:436
BINDING SITE FOR RESIDUE CL D1580
15
BC6
SOFTWARE
PRO D:151 , ARG D:161
BINDING SITE FOR RESIDUE ACT D1581
16
BC7
SOFTWARE
MET D:522 , ARG D:525
BINDING SITE FOR RESIDUE ACT D1582
17
BC8
SOFTWARE
PRO D:303 , ARG D:487
BINDING SITE FOR RESIDUE ACT D1583
18
BC9
SOFTWARE
PRO A:101 , GLU A:102 , PRO A:103 , HOH A:2098 , ARG C:148 , SER C:149 , PRO C:151 , HOH C:2041
BINDING SITE FOR LIGAND CSO C 150 BOUND TO SER C 149
19
CC1
SOFTWARE
ASN C:189 , ASN C:192 , LEU C:196 , ALA C:198 , VAL C:199 , GLN C:201 , HOH C:2069
BINDING SITE FOR MONO-SACCHARIDE NAG C1620 BOUND TO ASN C 189
20
CC2
SOFTWARE
ASN C:225 , SER C:227 , ALA C:228 , TRP C:369 , LEU C:373
BINDING SITE FOR MONO-SACCHARIDE NAG C1630 BOUND TO ASN C 225
21
CC3
SOFTWARE
TRP B:32 , LEU B:33 , ASN C:317 , VAL C:320 , ARG C:504 , HOH C:2148 , HOH C:2244 , HOH C:2246 , HOH C:2247 , HOH C:2248 , HOH C:2249 , HOH C:2250 , HOH C:2251 , HOH C:2253 , HOH C:2254 , LYS D:308 , PHE D:439 , GLY D:441 , LYS D:505 , MAN D:2644 , FUC D:2645
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG C1640 THROUGH FUC C1645 BOUND TO ASN C 317
22
CC4
SOFTWARE
PRO B:101 , GLU B:102 , PRO B:103 , HOH B:2098 , ARG D:148 , SER D:149 , PRO D:151 , GLN D:163
BINDING SITE FOR LIGAND CSO D 150 BOUND TO SER D 149
23
CC5
SOFTWARE
ASN D:189 , ASN D:192 , ALA D:198 , VAL D:199 , GLN D:201 , HOH D:2049 , HOH D:2051 , HOH D:2193
BINDING SITE FOR MONO-SACCHARIDE NAG D2620 BOUND TO ASN D 189
24
CC6
SOFTWARE
ASN D:225 , ALA D:228 , TRP D:369
BINDING SITE FOR MONO-SACCHARIDE NAG D2630 BOUND TO ASN D 225
25
CC7
SOFTWARE
TRP A:32 , LEU A:33 , HOH A:2044 , LYS C:308 , PHE C:439 , GLY C:441 , LYS C:505 , MAN C:1644 , FUC C:1645 , HOH C:2137 , HOH C:2186 , HOH C:2188 , HOH C:2253 , HOH C:2254 , ASN D:317 , SER D:319 , VAL D:320 , ARG D:504 , HOH D:2194
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG D2640 THROUGH FUC D2645 BOUND TO ASN D 317
[
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:4-17 | B:1-17 | - | -)
Exon 1.4c (A:17-60 | B:17-60 | - | -)
Exon 1.5 (A:61-105 | B:61-105 | 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:4-17
B:1-17
-
-
14
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:61-105
B:61-105
C:113-129
D:113-129
45
45
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:
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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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Asym.Unit (213 KB)
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