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4DL1
Biol. Unit 5
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Asym.Unit (1.6 MB)
Biol.Unit 1 (427 KB)
Biol.Unit 10 (218 KB)
Biol.Unit 11 (219 KB)
Biol.Unit 12 (222 KB)
Biol.Unit 2 (423 KB)
Biol.Unit 3 (420 KB)
Biol.Unit 4 (426 KB)
Biol.Unit 5 (221 KB)
Biol.Unit 6 (220 KB)
Biol.Unit 7 (219 KB)
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Biol.Unit 9 (217 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN MYELOPEROXIDASE WITH COVALENT THIOXANTHINE ANALOG
Authors
:
F. Vajdos, A. Varghese
Date
:
05 Feb 12 (Deposition) - 21 Mar 12 (Release) - 09 May 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Biol. Unit 3: I,J,K,L (1x)
Biol. Unit 4: M,N,O,P (1x)
Biol. Unit 5: A,C (1x)
Biol. Unit 6: B,D (1x)
Biol. Unit 7: E,G (1x)
Biol. Unit 8: F,H (1x)
Biol. Unit 9: I,K (1x)
Biol. Unit 10: J,L (1x)
Biol. Unit 11: M,O (1x)
Biol. Unit 12: N,P (1x)
Keywords
:
Oxidoreductase, Heme-Dependent Peroxidase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. F. Geoghegan, A. H. Varghese, X. Feng, A. J. Bessire, J. J. Conboy, R. B. Ruggeri, K. Ahn, S. N. Spath, S. V. Filippov, S. J. Conrad, P. A. Carpino, C. R. Guimaraes, F. F. Vajdos
Deconstruction Of Activity-Dependent Covalent Modification Of Heme In Human Neutrophil Myeloperoxidase By Multistage Mass Spectrometry (Ms(4)).
Biochemistry V. 51 2065 2012
[
close entry info
]
Hetero Components
(7, 11)
Info
All Hetero Components
1a: 3-[(2R)-2-ETHOXYPROPYL]-2-THIOXO-1... (0KYa)
1b: 3-[(2R)-2-ETHOXYPROPYL]-2-THIOXO-1... (0KYb)
1c: 3-[(2R)-2-ETHOXYPROPYL]-2-THIOXO-1... (0KYc)
1d: 3-[(2R)-2-ETHOXYPROPYL]-2-THIOXO-1... (0KYd)
1e: 3-[(2R)-2-ETHOXYPROPYL]-2-THIOXO-1... (0KYe)
1f: 3-[(2R)-2-ETHOXYPROPYL]-2-THIOXO-1... (0KYf)
1g: 3-[(2R)-2-ETHOXYPROPYL]-2-THIOXO-1... (0KYg)
1h: 3-[(2R)-2-ETHOXYPROPYL]-2-THIOXO-1... (0KYh)
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)
2g: BETA-D-MANNOSE (BMAg)
2h: BETA-D-MANNOSE (BMAh)
2i: BETA-D-MANNOSE (BMAi)
3a: CALCIUM ION (CAa)
3b: CALCIUM ION (CAb)
3c: CALCIUM ION (CAc)
3d: CALCIUM ION (CAd)
3e: CALCIUM ION (CAe)
3f: CALCIUM ION (CAf)
3g: CALCIUM ION (CAg)
3h: CALCIUM ION (CAh)
4a: CHLORIDE ION (CLa)
4b: CHLORIDE ION (CLb)
4c: CHLORIDE ION (CLc)
4d: CHLORIDE ION (CLd)
4e: CHLORIDE ION (CLe)
4f: CHLORIDE ION (CLf)
4g: CHLORIDE ION (CLg)
4h: CHLORIDE ION (CLh)
5a: S-HYDROXYCYSTEINE (CSOa)
5b: S-HYDROXYCYSTEINE (CSOb)
5c: S-HYDROXYCYSTEINE (CSOc)
5d: S-HYDROXYCYSTEINE (CSOd)
5e: S-HYDROXYCYSTEINE (CSOe)
5f: S-HYDROXYCYSTEINE (CSOf)
5g: S-HYDROXYCYSTEINE (CSOg)
5h: S-HYDROXYCYSTEINE (CSOh)
6a: ALPHA-L-FUCOSE (FUCa)
6b: ALPHA-L-FUCOSE (FUCb)
6c: ALPHA-L-FUCOSE (FUCc)
6d: ALPHA-L-FUCOSE (FUCd)
6e: ALPHA-L-FUCOSE (FUCe)
6f: ALPHA-L-FUCOSE (FUCf)
6g: ALPHA-L-FUCOSE (FUCg)
6h: ALPHA-L-FUCOSE (FUCh)
7a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
7b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
7c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
7d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
7e: PROTOPORPHYRIN IX CONTAINING FE (HEMe)
7f: PROTOPORPHYRIN IX CONTAINING FE (HEMf)
7g: PROTOPORPHYRIN IX CONTAINING FE (HEMg)
7h: PROTOPORPHYRIN IX CONTAINING FE (HEMh)
8a: ALPHA-D-MANNOSE (MANa)
8b: ALPHA-D-MANNOSE (MANb)
8c: ALPHA-D-MANNOSE (MANc)
8d: ALPHA-D-MANNOSE (MANd)
8e: ALPHA-D-MANNOSE (MANe)
8f: ALPHA-D-MANNOSE (MANf)
8g: ALPHA-D-MANNOSE (MANg)
8h: ALPHA-D-MANNOSE (MANh)
8i: ALPHA-D-MANNOSE (MANi)
8j: ALPHA-D-MANNOSE (MANj)
8k: ALPHA-D-MANNOSE (MANk)
8l: ALPHA-D-MANNOSE (MANl)
8m: ALPHA-D-MANNOSE (MANm)
8n: ALPHA-D-MANNOSE (MANn)
8o: ALPHA-D-MANNOSE (MANo)
8p: ALPHA-D-MANNOSE (MANp)
8q: ALPHA-D-MANNOSE (MANq)
8r: ALPHA-D-MANNOSE (MANr)
9a: N-ACETYL-D-GLUCOSAMINE (NAGa)
9aa: N-ACETYL-D-GLUCOSAMINE (NAGaa)
9ab: N-ACETYL-D-GLUCOSAMINE (NAGab)
9ac: N-ACETYL-D-GLUCOSAMINE (NAGac)
9ad: N-ACETYL-D-GLUCOSAMINE (NAGad)
9ae: N-ACETYL-D-GLUCOSAMINE (NAGae)
9af: N-ACETYL-D-GLUCOSAMINE (NAGaf)
9ag: N-ACETYL-D-GLUCOSAMINE (NAGag)
9b: N-ACETYL-D-GLUCOSAMINE (NAGb)
9c: N-ACETYL-D-GLUCOSAMINE (NAGc)
9d: N-ACETYL-D-GLUCOSAMINE (NAGd)
9e: N-ACETYL-D-GLUCOSAMINE (NAGe)
9f: N-ACETYL-D-GLUCOSAMINE (NAGf)
9g: N-ACETYL-D-GLUCOSAMINE (NAGg)
9h: N-ACETYL-D-GLUCOSAMINE (NAGh)
9i: N-ACETYL-D-GLUCOSAMINE (NAGi)
9j: N-ACETYL-D-GLUCOSAMINE (NAGj)
9k: N-ACETYL-D-GLUCOSAMINE (NAGk)
9l: N-ACETYL-D-GLUCOSAMINE (NAGl)
9m: N-ACETYL-D-GLUCOSAMINE (NAGm)
9n: N-ACETYL-D-GLUCOSAMINE (NAGn)
9o: N-ACETYL-D-GLUCOSAMINE (NAGo)
9p: N-ACETYL-D-GLUCOSAMINE (NAGp)
9q: N-ACETYL-D-GLUCOSAMINE (NAGq)
9r: N-ACETYL-D-GLUCOSAMINE (NAGr)
9s: N-ACETYL-D-GLUCOSAMINE (NAGs)
9t: N-ACETYL-D-GLUCOSAMINE (NAGt)
9u: N-ACETYL-D-GLUCOSAMINE (NAGu)
9v: N-ACETYL-D-GLUCOSAMINE (NAGv)
9w: N-ACETYL-D-GLUCOSAMINE (NAGw)
9x: N-ACETYL-D-GLUCOSAMINE (NAGx)
9y: N-ACETYL-D-GLUCOSAMINE (NAGy)
9z: N-ACETYL-D-GLUCOSAMINE (NAGz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
0KY
1
Ligand/Ion
3-[(2R)-2-ETHOXYPROPYL]-2-THIOXO-1,2,3,9-TETRAHYDRO-6H-PURIN-6-ONE
2
BMA
1
Ligand/Ion
BETA-D-MANNOSE
3
CA
-1
Ligand/Ion
CALCIUM ION
4
CL
-1
Ligand/Ion
CHLORIDE ION
5
CSO
1
Mod. Amino Acid
S-HYDROXYCYSTEINE
6
FUC
1
Ligand/Ion
ALPHA-L-FUCOSE
7
HEM
1
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
8
MAN
2
Ligand/Ion
ALPHA-D-MANNOSE
9
NAG
4
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(21, 21)
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: BC7 (SOFTWARE)
14: BC8 (SOFTWARE)
15: BC9 (SOFTWARE)
16: CC1 (SOFTWARE)
17: CC2 (SOFTWARE)
18: CC3 (SOFTWARE)
19: KC6 (SOFTWARE)
20: KC7 (SOFTWARE)
21: KC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:31 , TRP A:32 , HOH A:1704 , VAL C:327
BINDING SITE FOR RESIDUE CL A 1601
02
AC2
SOFTWARE
GLU A:102 , PRO A:103 , HOH A:1706 , HOH A:1741 , PHE C:147 , ARG C:239 , HEM C:601 , HOH C:702 , HOH C:835
BINDING SITE FOR RESIDUE 0KY A 1602
03
AC3
SOFTWARE
MET A:87 , GLY A:90 , GLN A:91 , ASP A:94 , ASP A:98 , PHE A:99 , THR A:100 , 0KY A:1602 , HOH A:1701 , ARG C:239 , GLU C:242 , MET C:243 , THR C:329 , PHE C:332 , ARG C:333 , GLY C:335 , HIS C:336 , LEU C:417 , ARG C:424 , HOH C:702 , HOH C:1035
BINDING SITE FOR RESIDUE HEM C 601
04
AC4
SOFTWARE
ASN C:317 , VAL C:320 , NAG C:603 , FUC C:607 , HOH C:836 , HOH C:853 , HOH D:814
BINDING SITE FOR RESIDUE NAG C 602
05
AC5
SOFTWARE
LEU B:33 , SER C:319 , NAG C:602 , BMA C:604 , HOH C:730 , HOH C:769 , HOH C:819 , HOH C:952 , PHE D:439 , GLY D:441 , HOH D:814
BINDING SITE FOR RESIDUE NAG C 603
06
AC6
SOFTWARE
NAG C:603 , MAN C:605 , MAN C:606 , HOH C:775 , PHE D:439 , HOH D:817
BINDING SITE FOR RESIDUE BMA C 604
07
AC7
SOFTWARE
BMA C:604 , HOH C:756 , LYS D:308
BINDING SITE FOR RESIDUE MAN C 605
08
AC8
SOFTWARE
BMA C:604 , HOH C:763 , HOH C:817 , PHE D:439 , LYS D:505 , FUC D:606
BINDING SITE FOR RESIDUE MAN C 606
09
AC9
SOFTWARE
ARG C:504 , NAG C:602 , HOH C:1007 , MAN D:605 , HOH D:915
BINDING SITE FOR RESIDUE FUC C 607
10
BC1
SOFTWARE
ASN C:189 , ASN C:192 , ALA C:198 , VAL C:199 , GLN C:201 , HOH C:825 , HOH C:1016
BINDING SITE FOR RESIDUE NAG C 608
11
BC2
SOFTWARE
ASN C:225 , TRP C:369
BINDING SITE FOR RESIDUE NAG C 609
12
BC3
SOFTWARE
ASP A:96 , THR C:168 , PHE C:170 , ASP C:172 , SER C:174
BINDING SITE FOR RESIDUE CA C 610
13
BC7
SOFTWARE
HOH C:721 , ASN D:317 , NAG D:602 , FUC D:606 , HOH D:716 , HOH D:819
BINDING SITE FOR RESIDUE NAG D 601
14
BC8
SOFTWARE
LEU A:33 , ARG C:438 , PHE C:439 , GLY C:441 , HOH C:721 , HOH C:948 , SER D:319 , NAG D:601 , BMA D:603 , FUC D:606 , HOH D:835 , HOH D:878 , HOH D:914
BINDING SITE FOR RESIDUE NAG D 602
15
BC9
SOFTWARE
PHE C:439 , HOH C:848 , NAG D:602 , MAN D:604 , MAN D:605
BINDING SITE FOR RESIDUE BMA D 603
16
CC1
SOFTWARE
LYS C:308 , BMA D:603
BINDING SITE FOR RESIDUE MAN D 604
17
CC2
SOFTWARE
PHE C:439 , LYS C:505 , FUC C:607 , HOH C:904 , HOH C:1007 , BMA D:603 , HOH D:915 , HOH D:939
BINDING SITE FOR RESIDUE MAN D 605
18
CC3
SOFTWARE
MAN C:606 , NAG D:601 , NAG D:602
BINDING SITE FOR RESIDUE FUC D 606
19
KC6
SOFTWARE
LEU C:194 , HOH C:869 , NAG P:609 , BMA P:611 , HOH P:836 , HOH P:862 , HOH P:874 , HOH P:886
BINDING SITE FOR RESIDUE NAG P 610
20
KC7
SOFTWARE
HOH C:869 , NAG P:610 , MAN P:612 , MAN P:613 , HOH P:862 , HOH P:874
BINDING SITE FOR RESIDUE BMA P 611
21
KC9
SOFTWARE
SER C:191 , BMA P:611
BINDING SITE FOR RESIDUE MAN P 613
[
close Site info
]
SAPs(SNPs)/Variants
(8, 8)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_015377 (Y7C, chain A, )
2: VAR_015378 (M85T, chain A, )
3: VAR_036517 (R281Q, chain C, )
4: VAR_PERM_HUMAN_CCDS11604_1_01 (R281Q, chain C, )
5: VAR_015379 (R403W, chain C, )
6: VAR_023996 (R438C, chain C, )
7: VAR_023997 (E517Q, chain C, )
8: VAR_012066 (I551V, chain C, )
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
Y
7
C
2
UniProt
VAR_015378
M
251
T
PERM_HUMAN
Disease (MPOD)
56378716
A
M
85
T
3
UniProt
VAR_036517
R
447
Q
PERM_HUMAN
Unclassified
---
C
R
281
Q
4
CancerSNP
VAR_PERM_HUMAN_CCDS11604_1_01
*
R
447
Q
PERM_HUMAN
Disease (Colorectal cancer)
---
C
R
281
Q
5
UniProt
VAR_015379
R
569
W
PERM_HUMAN
Disease (MPOD)
---
C
R
403
W
6
UniProt
VAR_023996
R
604
C
PERM_HUMAN
Polymorphism
35670089
C
R
438
C
7
UniProt
VAR_023997
E
683
Q
PERM_HUMAN
Polymorphism
35702888
C
E
517
Q
8
UniProt
VAR_012066
I
717
V
PERM_HUMAN
Polymorphism
2759
C
I
551
V
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: PEROXIDASE_1 (C: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
1
C:242-252
-
-
-
-
-
-
-
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
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All Exon Boundaries
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Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
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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:
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Label:
Sorry, no Info available
[
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(currently selected atoms:
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Asymmetric Unit 1
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