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1MHL
Biol. Unit 2
Info
Asym.Unit (207 KB)
Biol.Unit 1 (198 KB)
Biol.Unit 2 (102 KB)
Biol.Unit 3 (102 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN MYELOPEROXIDASE ISOFORM C CRYSTALLIZED IN SPACE GROUP P2(1) AT PH 5.5 AND 20 DEG C
Authors
:
R. E. Fenna, J. Zeng, C. Davey
Date
:
09 Jun 95 (Deposition) - 06 Jan 96 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.25
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
:
Myeloperoxidase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Fenna, J. Zeng, C. Davey
Structure Of The Green Heme In Myeloperoxidase.
Arch. Biochem. Biophys. V. 316 653 1995
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(5, 9)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
3a: CHLORIDE ION (CLa)
3b: CHLORIDE ION (CLb)
4a: ALPHA-L-FUCOSE (FUCa)
4b: ALPHA-L-FUCOSE (FUCb)
5a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
5b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
6a: ALPHA-D-MANNOSE (MANa)
6b: ALPHA-D-MANNOSE (MANb)
6c: ALPHA-D-MANNOSE (MANc)
6d: ALPHA-D-MANNOSE (MANd)
7a: N-ACETYL-D-GLUCOSAMINE (NAGa)
7b: N-ACETYL-D-GLUCOSAMINE (NAGb)
7c: N-ACETYL-D-GLUCOSAMINE (NAGc)
7d: N-ACETYL-D-GLUCOSAMINE (NAGd)
7e: N-ACETYL-D-GLUCOSAMINE (NAGe)
7f: N-ACETYL-D-GLUCOSAMINE (NAGf)
7g: N-ACETYL-D-GLUCOSAMINE (NAGg)
7h: N-ACETYL-D-GLUCOSAMINE (NAGh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
1
Ligand/Ion
BETA-D-MANNOSE
2
CA
-1
Ligand/Ion
CALCIUM ION
3
CL
-1
Ligand/Ion
CHLORIDE ION
4
FUC
1
Ligand/Ion
ALPHA-L-FUCOSE
5
HEM
1
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
6
MAN
2
Ligand/Ion
ALPHA-D-MANNOSE
7
NAG
4
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(16, 16)
Info
All Sites
01: AC4 (SOFTWARE)
02: AC5 (SOFTWARE)
03: AC6 (SOFTWARE)
04: AC7 (SOFTWARE)
05: AC8 (SOFTWARE)
06: AC9 (SOFTWARE)
07: BC1 (SOFTWARE)
08: BC2 (SOFTWARE)
09: BC3 (SOFTWARE)
10: BC4 (SOFTWARE)
11: BC5 (SOFTWARE)
12: BC6 (SOFTWARE)
13: BC7 (SOFTWARE)
14: CC1 (SOFTWARE)
15: CC2 (SOFTWARE)
16: CC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC4
SOFTWARE
NAG A:640 , BMA A:642 , HOH A:679 , HOH A:693 , HOH A:699 , LEU B:33 , SER C:319 , ARG D:438 , PHE D:439 , GLY D:441
BINDING SITE FOR RESIDUE NAG A 641
02
AC5
SOFTWARE
NAG A:641 , MAN A:643 , MAN A:644 , PHE D:439 , HOH D:668
BINDING SITE FOR RESIDUE BMA A 642
03
AC6
SOFTWARE
BMA A:642 , LYS D:308
BINDING SITE FOR RESIDUE MAN A 643
04
AC7
SOFTWARE
BMA A:642 , HOH A:700 , FUC B:645 , HOH B:697 , PHE D:439 , LYS D:505
BINDING SITE FOR RESIDUE MAN A 644
05
AC8
SOFTWARE
NAG A:640 , HOH A:692 , MAN B:644 , HOH B:648 , ARG C:504
BINDING SITE FOR RESIDUE FUC A 645
06
AC9
SOFTWARE
ASN D:189 , ASN D:192 , LEU D:194 , ALA D:198 , VAL D:199 , GLN D:201 , HOH D:617
BINDING SITE FOR RESIDUE NAG B 620
07
BC1
SOFTWARE
ASN D:225 , ALA D:228 , TRP D:369 , LEU D:373
BINDING SITE FOR RESIDUE NAG B 630
08
BC2
SOFTWARE
NAG B:641 , FUC B:645 , HOH C:735 , ASN D:317 , VAL D:320
BINDING SITE FOR RESIDUE NAG B 640
09
BC3
SOFTWARE
LEU A:33 , NAG B:640 , BMA B:642 , MAN B:643 , HOH B:646 , HOH B:698 , ARG C:438 , PHE C:439 , GLY C:441 , HOH C:735
BINDING SITE FOR RESIDUE NAG B 641
10
BC4
SOFTWARE
NAG B:641 , MAN B:643 , MAN B:644 , HOH B:647 , PHE C:439 , HOH C:669
BINDING SITE FOR RESIDUE BMA B 642
11
BC5
SOFTWARE
NAG B:641 , BMA B:642 , LYS C:308 , GLY C:441
BINDING SITE FOR RESIDUE MAN B 643
12
BC6
SOFTWARE
FUC A:645 , HOH A:692 , BMA B:642 , HOH B:648 , PHE C:439 , LYS C:505
BINDING SITE FOR RESIDUE MAN B 644
13
BC7
SOFTWARE
MAN A:644 , NAG B:640 , HOH B:697 , VAL D:320 , ARG D:504
BINDING SITE FOR RESIDUE FUC B 645
14
CC1
SOFTWARE
ASP B:96 , THR D:168 , PHE D:170 , ASP D:172 , SER D:174
BINDING SITE FOR RESIDUE CA B 601
15
CC2
SOFTWARE
ARG B:31 , TRP B:32 , VAL D:327
BINDING SITE FOR RESIDUE CL B 602
16
CC4
SOFTWARE
MET B:87 , GLY B:90 , GLN B:91 , ASP B:94 , ASP B:98 , PHE B:99 , THR B:100 , HOH B:650 , HOH B:651 , HOH B:695 , 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
View:
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All Exon Boundaries
View:
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_d1mhl_1 (A:,C:)
1b: SCOP_d1mhl_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
d1mhl.1
A:,C:
1b
d1mhl.2
B:,D:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1mhlC00 (C:113-578)
1b: CATH_1mhlD00 (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
1mhlC00
C:113-578
1b
1mhlD00
D:113-578
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_An_peroxidase_1mhlD01 (D:113-552)
1b: PFAM_An_peroxidase_1mhlD02 (D:113-552)
1c: PFAM_An_peroxidase_1mhlD03 (D:113-552)
1d: PFAM_An_peroxidase_1mhlD04 (D:113-552)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: An_peroxidase]
(45)
Family
:
An_peroxidase
(45)
Homo sapiens (Human)
(2)
1a
An_peroxidase-1mhlD01
D:113-552
1b
An_peroxidase-1mhlD02
D:113-552
1c
An_peroxidase-1mhlD03
D:113-552
1d
An_peroxidase-1mhlD04
D:113-552
[
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]
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