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1DNW
Biol. Unit 2
Info
Asym.Unit (217 KB)
Biol.Unit 1 (208 KB)
Biol.Unit 2 (107 KB)
Biol.Unit 3 (108 KB)
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Title
:
HUMAN MYELOPEROXIDASE-CYANIDE-THIOCYANATE COMPLEX
Authors
:
M. Blair-Johnson, T. J. Fiedler, R. E. Fenna
Date
:
16 Dec 99 (Deposition) - 21 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: A,C (1x)
Biol. Unit 3: B,D (1x)
Keywords
:
Oxidoreductase, Peroxidase, Substrate Complex, Thiocyanate, Halide Peroxidation
(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
[
close entry info
]
Hetero Components
(10, 19)
Info
All Hetero Components
01a: ACETIC ACID (ACYa)
01b: ACETIC ACID (ACYb)
01c: ACETIC ACID (ACYc)
01d: ACETIC ACID (ACYd)
01e: ACETIC ACID (ACYe)
01f: ACETIC ACID (ACYf)
02a: BETA-D-MANNOSE (BMAa)
02b: BETA-D-MANNOSE (BMAb)
03a: CALCIUM ION (CAa)
03b: CALCIUM ION (CAb)
04a: S-HYDROXYCYSTEINE (CSOa)
04b: S-HYDROXYCYSTEINE (CSOb)
05a: CYANIDE ION (CYNa)
05b: CYANIDE ION (CYNb)
05c: CYANIDE ION (CYNc)
05d: CYANIDE ION (CYNd)
06a: ALPHA-L-FUCOSE (FUCa)
06b: ALPHA-L-FUCOSE (FUCb)
07a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
07b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
08a: ALPHA-D-MANNOSE (MANa)
08b: ALPHA-D-MANNOSE (MANb)
08c: ALPHA-D-MANNOSE (MANc)
08d: ALPHA-D-MANNOSE (MANd)
09a: N-ACETYL-D-GLUCOSAMINE (NAGa)
09b: N-ACETYL-D-GLUCOSAMINE (NAGb)
09c: N-ACETYL-D-GLUCOSAMINE (NAGc)
09d: N-ACETYL-D-GLUCOSAMINE (NAGd)
09e: N-ACETYL-D-GLUCOSAMINE (NAGe)
09f: N-ACETYL-D-GLUCOSAMINE (NAGf)
09g: N-ACETYL-D-GLUCOSAMINE (NAGg)
09h: N-ACETYL-D-GLUCOSAMINE (NAGh)
10a: THIOCYANATE ION (SCNa)
10b: THIOCYANATE ION (SCNb)
10c: THIOCYANATE ION (SCNc)
10d: THIOCYANATE ION (SCNd)
11a: SULFATE ION (SO4a)
11b: SULFATE ION (SO4b)
11c: SULFATE ION (SO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACY
3
Ligand/Ion
ACETIC ACID
2
BMA
1
Ligand/Ion
BETA-D-MANNOSE
3
CA
-1
Ligand/Ion
CALCIUM ION
4
CSO
1
Mod. Amino Acid
S-HYDROXYCYSTEINE
5
CYN
2
Ligand/Ion
CYANIDE ION
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
SCN
2
Ligand/Ion
THIOCYANATE ION
11
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: BC2 (SOFTWARE)
10: BC3 (SOFTWARE)
11: BC4 (SOFTWARE)
12: BC5 (SOFTWARE)
13: BC6 (SOFTWARE)
14: BC7 (SOFTWARE)
15: BC8 (SOFTWARE)
16: BC9 (SOFTWARE)
17: CC1 (SOFTWARE)
18: CC2 (SOFTWARE)
19: CC3 (SOFTWARE)
20: CC4 (SOFTWARE)
21: CC5 (SOFTWARE)
22: DC3 (SOFTWARE)
23: DC5 (SOFTWARE)
24: DC6 (SOFTWARE)
25: DC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN C:189 , ASN C:192 , ALA C:198 , VAL C:199 , GLN C:201 , HOH C:695 , HOH C:891 , HOH C:892
BINDING SITE FOR RESIDUE NAG C 620
02
AC2
SOFTWARE
ASN C:225 , ALA C:228 , TRP C:369
BINDING SITE FOR RESIDUE NAG C 630
03
AC3
SOFTWARE
ASN C:317 , VAL C:320 , NAG C:641 , FUC C:645 , HOH C:649 , HOH C:795 , HOH D:647
BINDING SITE FOR RESIDUE NAG C 640
04
AC4
SOFTWARE
LEU B:33 , SER C:319 , NAG C:640 , BMA C:642 , HOH C:755 , HOH C:817 , ARG D:438 , PHE D:439 , GLY D:441 , HOH D:647 , HOH D:702
BINDING SITE FOR RESIDUE NAG C 641
05
AC5
SOFTWARE
NAG C:641 , MAN C:643 , MAN C:644 , HOH C:973 , PHE D:439 , HOH D:752
BINDING SITE FOR RESIDUE BMA C 642
06
AC6
SOFTWARE
BMA C:642 , LYS D:308
BINDING SITE FOR RESIDUE MAN C 643
07
AC7
SOFTWARE
TRP B:32 , BMA C:642 , HOH C:817 , HOH C:976 , HOH C:979 , PHE D:439 , LYS D:505 , FUC D:645
BINDING SITE FOR RESIDUE MAN C 644
08
AC8
SOFTWARE
ARG C:504 , NAG C:640 , HOH C:773 , MAN D:644 , HOH D:649 , HOH D:651
BINDING SITE FOR RESIDUE FUC C 645
09
BC2
SOFTWARE
HOH C:974 , ASN D:317 , VAL D:320 , NAG D:641 , FUC D:645 , HOH D:661 , HOH D:809
BINDING SITE FOR RESIDUE NAG D 640
10
BC3
SOFTWARE
LEU A:33 , ARG C:438 , PHE C:439 , GLY C:441 , HOH C:687 , HOH C:974 , SER D:319 , NAG D:640 , BMA D:642 , HOH D:769 , HOH D:839
BINDING SITE FOR RESIDUE NAG D 641
11
BC4
SOFTWARE
PHE C:439 , HOH C:735 , NAG D:641 , MAN D:643 , MAN D:644 , HOH D:646
BINDING SITE FOR RESIDUE BMA D 642
12
BC5
SOFTWARE
LYS C:308 , BMA D:642
BINDING SITE FOR RESIDUE MAN D 643
13
BC6
SOFTWARE
TRP A:32 , PHE C:439 , LYS C:505 , FUC C:645 , BMA D:642 , HOH D:649 , HOH D:651 , HOH D:657 , HOH D:831
BINDING SITE FOR RESIDUE MAN D 644
14
BC7
SOFTWARE
MAN C:644 , HOH C:976 , HOH C:979 , ARG D:504 , NAG D:640 , HOH D:788
BINDING SITE FOR RESIDUE FUC D 645
15
BC8
SOFTWARE
ASP A:96 , THR C:168 , PHE C:170 , ASP C:172 , SER C:174
BINDING SITE FOR RESIDUE CA C 1
16
BC9
SOFTWARE
ARG A:31 , TRP A:32 , LEU A:33 , ASN C:326 , VAL C:327 , LEU C:430 , TRP C:436
BINDING SITE FOR RESIDUE SCN A 105
17
CC1
SOFTWARE
THR A:73 , HOH A:185 , HOH A:190 , ASP C:400 , ARG C:405 , HOH C:781
BINDING SITE FOR RESIDUE SO4 A 106
18
CC2
SOFTWARE
ARG C:229 , THR C:447 , GLY C:449 , GLN C:450
BINDING SITE FOR RESIDUE SO4 C 13
19
CC3
SOFTWARE
GLN A:91 , HIS A:95 , CYN A:107 , HEM C:14 , ARG C:239 , GLU C:242 , HOH C:866
BINDING SITE FOR RESIDUE SCN C 9
20
CC4
SOFTWARE
GLN A:91 , HIS A:95 , SCN C:9 , HEM C:14
BINDING SITE FOR RESIDUE CYN A 107
21
CC5
SOFTWARE
ASN C:200 , GLN C:201 , PHE C:213
BINDING SITE FOR RESIDUE CYN C 6
22
DC3
SOFTWARE
MET A:87 , GLY A:90 , GLN A:91 , ASP A:94 , ASP A:98 , PHE A:99 , THR A:100 , CYN A:107 , SCN C:9 , 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:407 , LEU C:417 , ARG C:424 , HOH C:751 , HOH C:783
BINDING SITE FOR RESIDUE HEM C 14
23
DC5
SOFTWARE
PRO C:123 , ARG C:161 , HOH C:657 , HOH C:966
BINDING SITE FOR RESIDUE ACY C 19
24
DC6
SOFTWARE
ARG C:525
BINDING SITE FOR RESIDUE ACY C 21
25
DC7
SOFTWARE
PRO C:303 , ARG C:307 , ARG C:487
BINDING SITE FOR RESIDUE ACY C 20
[
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_d1dnw_1 (A:,C:)
1b: SCOP_d1dnw_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
d1dnw.1
A:,C:
1b
d1dnw.2
B:,D:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1dnwC00 (C:113-578)
1b: CATH_1dnwD00 (D:113-578)
View:
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Classes
(
)
(
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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
1dnwC00
C:113-578
1b
1dnwD00
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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Protein & NOT PROSITE
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Chain C
Asymmetric Unit 1
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