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1D5L
Biol. Unit 2
Info
Asym.Unit (217 KB)
Biol.Unit 1 (209 KB)
Biol.Unit 2 (108 KB)
Biol.Unit 3 (108 KB)
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Title
:
CRYSTAL STRUCTURE OF CYANIDE-BOUND HUMAN MYELOPEROXIDASE ISOFORM C AT PH 5.5
Authors
:
T. J. Fiedler, C. A. Davey, R. E. Fenna
Date
:
07 Oct 99 (Deposition) - 12 Dec 01 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
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, Peroxidase-Cyanide Complex, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Blair-Johnson, T. Fiedler, R. Fenna
Human Myeloperoxidase: Structure Of A Cyanide Complex And Its Interaction With Bromide And Thiocyanate Substrates At 1. 9 A Resolution.
Biochemistry V. 40 13990 2001
(for further references see the
PDB file header
)
[
close entry info
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Hetero Components
(9, 16)
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)
1g: ACETATE ION (ACTg)
2a: BETA-D-MANNOSE (BMAa)
2b: BETA-D-MANNOSE (BMAb)
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: CYANIDE ION (CYNa)
6b: CYANIDE ION (CYNb)
6c: CYANIDE ION (CYNc)
6d: CYANIDE ION (CYNd)
7a: ALPHA-L-FUCOSE (FUCa)
7b: ALPHA-L-FUCOSE (FUCb)
8a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
8b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
9a: ALPHA-D-MANNOSE (MANa)
9b: ALPHA-D-MANNOSE (MANb)
9c: ALPHA-D-MANNOSE (MANc)
9d: 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: SULFATE ION (SO4a)
11b: SULFATE ION (SO4b)
11c: 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
CA
-1
Ligand/Ion
CALCIUM ION
4
CL
-1
Ligand/Ion
CHLORIDE ION
5
CSO
1
Mod. Amino Acid
S-HYDROXYCYSTEINE
6
CYN
2
Ligand/Ion
CYANIDE ION
7
FUC
1
Ligand/Ion
ALPHA-L-FUCOSE
8
HEM
1
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
9
MAN
2
Ligand/Ion
ALPHA-D-MANNOSE
10
NAG
4
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
11
SO4
1
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(23, 23)
Info
All Sites
01: AC3 (SOFTWARE)
02: AC4 (SOFTWARE)
03: AC5 (SOFTWARE)
04: AC6 (SOFTWARE)
05: AC7 (SOFTWARE)
06: AC8 (SOFTWARE)
07: AC9 (SOFTWARE)
08: BC1 (SOFTWARE)
09: BC2 (SOFTWARE)
10: BC3 (SOFTWARE)
11: BC4 (SOFTWARE)
12: BC5 (SOFTWARE)
13: BC6 (SOFTWARE)
14: BC7 (SOFTWARE)
15: CC8 (SOFTWARE)
16: CC9 (SOFTWARE)
17: DC1 (SOFTWARE)
18: DC2 (SOFTWARE)
19: DC3 (SOFTWARE)
20: DC4 (SOFTWARE)
21: DC5 (SOFTWARE)
22: DC6 (SOFTWARE)
23: DC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC3
SOFTWARE
ASN C:317 , VAL C:320 , HOH C:651A , HOH C:861A , NAG C:1641 , FUC C:1645 , HOH D:775A
BINDING SITE FOR RESIDUE NAG C 1640
02
AC4
SOFTWARE
LEU B:33 , SER C:319 , HOH C:804A , NAG C:1640 , BMA C:1642 , PHE D:439 , GLY D:441 , HOH D:706B
BINDING SITE FOR RESIDUE NAG C 1641
03
AC5
SOFTWARE
HOH C:770B , NAG C:1641 , MAN C:1643 , MAN C:1644 , PHE D:439 , HOH D:771B
BINDING SITE FOR RESIDUE BMA C 1642
04
AC6
SOFTWARE
BMA C:1642 , LYS D:308
BINDING SITE FOR RESIDUE MAN C 1643
05
AC7
SOFTWARE
TRP B:32 , HOH C:888A , HOH C:923B , BMA C:1642 , PHE D:439 , LYS D:505 , HOH D:803B , FUC D:2645
BINDING SITE FOR RESIDUE MAN C 1644
06
AC8
SOFTWARE
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
AC9
SOFTWARE
ASN D:189 , ASN D:192 , ALA D:198 , VAL D:199 , GLN D:201 , HOH D:721B , HOH D:988B , HOH D:989B
BINDING SITE FOR RESIDUE NAG D 2620
08
BC1
SOFTWARE
ASN D:225 , ALA D:228 , TRP D:369
BINDING SITE FOR RESIDUE NAG D 2630
09
BC2
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
10
BC3
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
11
BC4
SOFTWARE
PHE C:439 , HOH C:770A , HOH C:771A , NAG D:2641 , MAN D:2643 , MAN D:2644
BINDING SITE FOR RESIDUE BMA D 2642
12
BC5
SOFTWARE
LYS C:308 , BMA D:2642
BINDING SITE FOR RESIDUE MAN D 2643
13
BC6
SOFTWARE
TRP A:32 , PHE C:439 , LYS C:505 , FUC C:1645 , HOH D:803A , HOH D:888B , HOH D:923A , HOH D:1263A , BMA D:2642
BINDING SITE FOR RESIDUE MAN D 2644
14
BC7
SOFTWARE
HOH C:923B , MAN C:1644 , VAL D:320 , ARG D:504 , HOH D:803B , HOH D:830B , NAG D:2640
BINDING SITE FOR RESIDUE FUC D 2645
15
CC8
SOFTWARE
ASP B:96 , THR D:168 , PHE D:170 , ASP D:172 , SER D:174
BINDING SITE FOR RESIDUE CA D 2600
16
CC9
SOFTWARE
ARG B:31 , TRP B:32 , ASN D:326 , VAL D:327 , TRP D:436
BINDING SITE FOR RESIDUE CL B 2601
17
DC1
SOFTWARE
THR B:73 , HOH B:961B , ARG D:405 , HOH D:842B
BINDING SITE FOR RESIDUE SO4 D 2602
18
DC2
SOFTWARE
PRO D:124 , ARG D:161 , HOH D:661B , HOH D:981B , HOH D:1278B
BINDING SITE FOR RESIDUE ACT D 2606
19
DC3
SOFTWARE
ARG D:525
BINDING SITE FOR RESIDUE ACT D 2604
20
DC4
SOFTWARE
PRO D:303 , ARG D:307 , ARG D:487 , LYS D:488
BINDING SITE FOR RESIDUE ACT D 2607
21
DC5
SOFTWARE
GLN B:91 , HIS B:95 , HEM B:605 , HOH B:843B , HOH B:845B
BINDING SITE FOR RESIDUE CYN B 2844
22
DC6
SOFTWARE
ASN D:200 , GLN D:201 , PHE D:213
BINDING SITE FOR RESIDUE CYN D 2889
23
DC8
SOFTWARE
MET B:87 , GLY B:90 , GLN B:91 , ASP B:94 , ASP B:98 , PHE B:99 , THR B:100 , HOH B:798B , HOH B:846B , HOH B:856B , CYN B:2844 , 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
[
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 B, )
2: VAR_015378 (M85T, chain B, )
3: VAR_036517 (R281Q, chain D, )
4: VAR_PERM_HUMAN_CCDS11604_1_01 (R281Q, chain D, )
5: VAR_015379 (R403W, chain D, )
6: VAR_023996 (R438C, chain D, )
7: VAR_023997 (E517Q, chain D, )
8: VAR_012066 (I551V, chain 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
B
Y
7
C
2
UniProt
VAR_015378
M
251
T
PERM_HUMAN
Disease (MPOD)
56378716
B
M
85
T
3
UniProt
VAR_036517
R
447
Q
PERM_HUMAN
Unclassified
---
D
R
281
Q
4
CancerSNP
VAR_PERM_HUMAN_CCDS11604_1_01
*
R
447
Q
PERM_HUMAN
Disease (Colorectal cancer)
---
D
R
281
Q
5
UniProt
VAR_015379
R
569
W
PERM_HUMAN
Disease (MPOD)
---
D
R
403
W
6
UniProt
VAR_023996
R
604
C
PERM_HUMAN
Polymorphism
35670089
D
R
438
C
7
UniProt
VAR_023997
E
683
Q
PERM_HUMAN
Polymorphism
35702888
D
E
517
Q
8
UniProt
VAR_012066
I
717
V
PERM_HUMAN
Polymorphism
2759
D
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 (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
1
-
D: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_d1d5l_1 (A:,C:)
1b: SCOP_d1d5l_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
d1d5l.1
A:,C:
1b
d1d5l.2
B:,D:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1d5lC00 (C:113-578)
1b: CATH_1d5lD00 (D:113-578)
View:
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Label:
Classes
(
)
(
)
Architectures
(
)
(
)
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
1d5lC00
C:113-578
1b
1d5lD00
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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Chain D
Asymmetric Unit 1
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