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1D2V
Biol. Unit 3
Info
Asym.Unit (216 KB)
Biol.Unit 1 (208 KB)
Biol.Unit 2 (108 KB)
Biol.Unit 3 (107 KB)
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Title
:
CRYSTAL STRUCTURE OF BROMIDE-BOUND HUMAN MYELOPEROXIDASE ISOFORM C AT PH 5.5
Authors
:
T. J. Fiedler, C. A. Davey, R. E. Fenna
Date
:
28 Sep 99 (Deposition) - 24 Apr 00 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.75
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: B,D (1x)
Biol. Unit 3: A,C (1x)
Keywords
:
Heme-Protein, Peroxidase, Oxidoreductase, Peroxidase-Bromide Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. J. Fiedler, C. A. Davey, R. E. Fenna
X-Ray Crystal Structure And Characterization Of Halide-Binding Sites Of Human Myeloperoxidase At 1. 8 A Resolution.
J. Biol. Chem. V. 275 11964 2000
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(8, 15)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
1e: ACETATE ION (ACTe)
1f: ACETATE ION (ACTf)
2a: BETA-D-MANNOSE (BMAa)
2b: BETA-D-MANNOSE (BMAb)
3a: BROMIDE ION (BRa)
3b: BROMIDE ION (BRb)
3c: BROMIDE ION (BRc)
3d: BROMIDE ION (BRd)
3e: BROMIDE ION (BRe)
3f: BROMIDE ION (BRf)
3g: BROMIDE ION (BRg)
3h: BROMIDE ION (BRh)
4a: CALCIUM ION (CAa)
4b: CALCIUM ION (CAb)
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: ALPHA-D-MANNOSE (MANa)
8b: ALPHA-D-MANNOSE (MANb)
8c: ALPHA-D-MANNOSE (MANc)
8d: ALPHA-D-MANNOSE (MANd)
9a: N-ACETYL-D-GLUCOSAMINE (NAGa)
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)
10a: SULFATE ION (SO4a)
10b: SULFATE ION (SO4b)
10c: SULFATE ION (SO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
3
Ligand/Ion
ACETATE ION
2
BMA
1
Ligand/Ion
BETA-D-MANNOSE
3
BR
-1
Ligand/Ion
BROMIDE ION
4
CA
-1
Ligand/Ion
CALCIUM 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
10
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: BC8 (SOFTWARE)
16: BC9 (SOFTWARE)
17: CC1 (SOFTWARE)
18: CC2 (SOFTWARE)
19: CC3 (SOFTWARE)
20: CC9 (SOFTWARE)
21: DC1 (SOFTWARE)
22: DC2 (SOFTWARE)
23: DC3 (SOFTWARE)
24: DC4 (SOFTWARE)
25: DC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN C:317 , VAL C:320 , HOH C:651A , NAG C:1641 , FUC C:1645 , HOH D:775A
BINDING SITE FOR RESIDUE NAG C 1640
02
AC2
SOFTWARE
LEU B:33 , SER C:319 , HOH C:804A , HOH C:888A , HOH C:897A , NAG C:1640 , BMA C:1642 , ARG D:438 , PHE D:439 , GLY D:441 , HOH D:706B , HOH D:775A
BINDING SITE FOR RESIDUE NAG C 1641
03
AC3
SOFTWARE
HOH C:770B , HOH C:888A , NAG C:1641 , MAN C:1643 , MAN C:1644 , PHE D:439 , HOH D:771B
BINDING SITE FOR RESIDUE BMA C 1642
04
AC4
SOFTWARE
BMA C:1642 , LYS D:308
BINDING SITE FOR RESIDUE MAN C 1643
05
AC5
SOFTWARE
HOH C:803B , HOH C:888A , HOH C:923B , BMA C:1642 , PHE D:439 , LYS D:505 , FUC D:2645
BINDING SITE FOR RESIDUE MAN C 1644
06
AC6
SOFTWARE
VAL C:320 , ARG C:504 , HOH C:830A , NAG C:1640 , HOH D:803A , HOH D:923A , MAN D:2644
BINDING SITE FOR RESIDUE FUC C 1645
07
AC7
SOFTWARE
HOH C:775B , ASN D:317 , VAL D:320 , HOH D:651B , HOH D:861B , NAG D:2641 , FUC D:2645
BINDING SITE FOR RESIDUE NAG D 2640
08
AC8
SOFTWARE
LEU A:33 , ARG C:438 , PHE C:439 , GLY C:441 , HOH C:775B , SER D:319 , HOH D:706A , HOH D:804B , HOH D:897B , NAG D:2640 , BMA D:2642
BINDING SITE FOR RESIDUE NAG D 2641
09
AC9
SOFTWARE
PHE C:439 , HOH C:770A , HOH D:771A , NAG D:2641 , MAN D:2643 , MAN D:2644
BINDING SITE FOR RESIDUE BMA D 2642
10
BC1
SOFTWARE
LYS C:308 , BMA D:2642
BINDING SITE FOR RESIDUE MAN D 2643
11
BC2
SOFTWARE
TRP A:32 , PHE C:439 , LYS C:505 , FUC C:1645 , HOH D:803A , HOH D:888B , HOH D:923A , BMA D:2642
BINDING SITE FOR RESIDUE MAN D 2644
12
BC3
SOFTWARE
HOH C:923B , MAN C:1644 , ARG D:504 , HOH D:830B , NAG D:2640
BINDING SITE FOR RESIDUE FUC D 2645
13
BC4
SOFTWARE
ASN C:189 , ASN C:192 , LEU C:196 , ALA C:198 , VAL C:199 , GLN C:201 , HOH C:721A , HOH C:1210A , HOH C:1250A
BINDING SITE FOR RESIDUE NAG C 1620
14
BC5
SOFTWARE
ASN C:225 , ALA C:228 , TRP C:369 , LEU C:373
BINDING SITE FOR RESIDUE NAG C 1630
15
BC8
SOFTWARE
ASP A:96 , THR C:168 , PHE C:170 , ASP C:172 , SER C:174
BINDING SITE FOR RESIDUE CA A 600
16
BC9
SOFTWARE
TRP A:32 , ASN C:326 , VAL C:327 , TRP C:436
BINDING SITE FOR RESIDUE BR A 601
17
CC1
SOFTWARE
ASN C:348 , ARG C:382 , ILE C:543 , THR C:544
BINDING SITE FOR RESIDUE BR A 758
18
CC2
SOFTWARE
GLN A:91 , HIS A:95 , GLU C:242 , HOH C:957A
BINDING SITE FOR RESIDUE BR A 843
19
CC3
SOFTWARE
ASN C:200 , GLN C:201 , PHE C:213
BINDING SITE FOR RESIDUE BR A 889
20
CC9
SOFTWARE
THR A:73 , HOH A:961A , HOH A:1223A , ASP C:400 , ARG C:405 , HOH C:842A
BINDING SITE FOR RESIDUE SO4 A 1602
21
DC1
SOFTWARE
ARG C:229 , THR C:447 , GLY C:449 , GLN C:450
BINDING SITE FOR RESIDUE SO4 C 1603
22
DC2
SOFTWARE
PRO C:123 , PRO C:124 , ARG C:161 , HOH C:661A , HOH C:871A , HOH C:1269A , HOH C:1281A
BINDING SITE FOR RESIDUE ACT C 1606
23
DC3
SOFTWARE
MET C:522 , ARG C:525
BINDING SITE FOR RESIDUE ACT C 1604
24
DC4
SOFTWARE
PRO C:303 , ARG C:487
BINDING SITE FOR RESIDUE ACT C 1607
25
DC9
SOFTWARE
MET A:87 , GLY A:90 , GLN A:91 , ASP A:94 , ASP A:98 , PHE A:99 , THR A:100 , HOH A:798A , HOH A:844A , HOH A:846A , ARG C:239 , GLU C:242 , MET C:243 , THR C:329 , PHE C:332 , ARG C:333 , GLY C:335 , HIS C:336 , PHE C:407 , LEU C:417 , LEU C:420 , ARG C:424
BINDING SITE FOR RESIDUE HEM A 605
[
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
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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
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1d2v_1 (A:,C:)
1b: SCOP_d1d2v_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)
Human (Homo sapiens) [TaxId: 9606]
(7)
1a
d1d2v.1
A:,C:
1b
d1d2v.2
B:,D:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1d2vC00 (C:113-578)
1b: CATH_1d2vD00 (D:113-578)
View:
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Classes
(
)
(
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(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Myeloperoxidase, subunit C
(39)
Homologous Superfamily
:
Myeloperoxidase, subunit C
(39)
Human (Homo sapiens)
(7)
1a
1d2vC00
C:113-578
1b
1d2vD00
D:113-578
[
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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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Atom Selection
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Asymmetric Unit 1
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