PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
Getting 'PROSITE' information from database.
1DNU
Biol. Unit 2
Info
Asym.Unit (216 KB)
Biol.Unit 1 (208 KB)
Biol.Unit 2 (107 KB)
Biol.Unit 3 (106 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURAL ANALYSES OF HUMAN MYELOPEROXIDASE-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
:
1.85
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
:
Oxidoreductase, Peroxidase, Inhibitor Complex Thiocyanate, Halide Peroxidation, Neutrophil
(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
(9, 16)
Info
All Hetero Components
1a: ACETIC ACID (ACYa)
1b: ACETIC ACID (ACYb)
1c: ACETIC ACID (ACYc)
1d: ACETIC ACID (ACYd)
1e: ACETIC ACID (ACYe)
1f: ACETIC ACID (ACYf)
2a: BETA-D-MANNOSE (BMAa)
2b: BETA-D-MANNOSE (BMAb)
3a: CALCIUM ION (CAa)
3b: CALCIUM ION (CAb)
4a: S-HYDROXYCYSTEINE (CSOa)
4b: S-HYDROXYCYSTEINE (CSOb)
5a: ALPHA-L-FUCOSE (FUCa)
5b: ALPHA-L-FUCOSE (FUCb)
6a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
6b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
7a: ALPHA-D-MANNOSE (MANa)
7b: ALPHA-D-MANNOSE (MANb)
7c: ALPHA-D-MANNOSE (MANc)
7d: ALPHA-D-MANNOSE (MANd)
8a: N-ACETYL-D-GLUCOSAMINE (NAGa)
8b: N-ACETYL-D-GLUCOSAMINE (NAGb)
8c: N-ACETYL-D-GLUCOSAMINE (NAGc)
8d: N-ACETYL-D-GLUCOSAMINE (NAGd)
8e: N-ACETYL-D-GLUCOSAMINE (NAGe)
8f: N-ACETYL-D-GLUCOSAMINE (NAGf)
8g: N-ACETYL-D-GLUCOSAMINE (NAGg)
8h: N-ACETYL-D-GLUCOSAMINE (NAGh)
9a: THIOCYANATE ION (SCNa)
9b: THIOCYANATE ION (SCNb)
9c: THIOCYANATE ION (SCNc)
9d: THIOCYANATE ION (SCNd)
10a: SULFATE ION (SO4a)
10b: SULFATE ION (SO4b)
10c: 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
FUC
1
Ligand/Ion
ALPHA-L-FUCOSE
6
HEM
1
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
7
MAN
2
Ligand/Ion
ALPHA-D-MANNOSE
8
NAG
4
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
9
SCN
2
Ligand/Ion
THIOCYANATE ION
10
SO4
1
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(22, 22)
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: CC4 (SOFTWARE)
16: CC5 (SOFTWARE)
17: CC6 (SOFTWARE)
18: CC7 (SOFTWARE)
19: CC9 (SOFTWARE)
20: DC4 (SOFTWARE)
21: DC5 (SOFTWARE)
22: DC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC3
SOFTWARE
ASN C:317 , VAL C:320 , NAG C:641 , FUC C:645 , HOH C:646 , HOH C:797 , HOH D:647
BINDING SITE FOR RESIDUE NAG C 640
02
AC4
SOFTWARE
LEU B:33 , SER C:319 , NAG C:640 , BMA C:642 , HOH C:756 , HOH C:967 , ARG D:438 , PHE D:439 , GLY D:441 , HOH D:647
BINDING SITE FOR RESIDUE NAG C 641
03
AC5
SOFTWARE
NAG C:641 , MAN C:643 , MAN C:644 , HOH C:968 , PHE D:439 , HOH D:747
BINDING SITE FOR RESIDUE BMA C 642
04
AC6
SOFTWARE
BMA C:642 , LYS D:308
BINDING SITE FOR RESIDUE MAN C 643
05
AC7
SOFTWARE
TRP B:32 , BMA C:642 , HOH C:973 , PHE D:439 , LYS D:505 , FUC D:645 , HOH D:766
BINDING SITE FOR RESIDUE MAN C 644
06
AC8
SOFTWARE
ARG C:504 , NAG C:640 , HOH C:773 , MAN D:644 , HOH D:649 , HOH D:652
BINDING SITE FOR RESIDUE FUC C 645
07
AC9
SOFTWARE
ASN D:189 , ASN D:192 , ALA D:198 , VAL D:199 , GLN D:201 , HOH D:707
BINDING SITE FOR RESIDUE NAG D 620
08
BC1
SOFTWARE
ASN D:225 , ALA D:228 , TRP D:369
BINDING SITE FOR RESIDUE NAG D 630
09
BC2
SOFTWARE
HOH C:969 , ASN D:317 , VAL D:320 , NAG D:641 , FUC D:645 , HOH D:660 , HOH D:805
BINDING SITE FOR RESIDUE NAG D 640
10
BC3
SOFTWARE
LEU A:33 , ARG C:438 , PHE C:439 , GLY C:441 , HOH C:969 , SER D:319 , NAG D:640 , BMA D:642 , HOH D:646 , HOH D:767 , HOH D:835
BINDING SITE FOR RESIDUE NAG D 641
11
BC4
SOFTWARE
PHE C:439 , HOH C:735 , HOH C:736 , NAG D:641 , MAN D:643 , MAN D:644
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:652 , HOH D:657 , HOH D:826
BINDING SITE FOR RESIDUE MAN D 644
14
BC7
SOFTWARE
MAN C:644 , HOH C:973 , ARG D:504 , NAG D:640 , HOH D:766 , HOH D:784
BINDING SITE FOR RESIDUE FUC D 645
15
CC4
SOFTWARE
ASP B:96 , THR D:168 , PHE D:170 , ASP D:172 , SER D:174
BINDING SITE FOR RESIDUE CA D 2
16
CC5
SOFTWARE
ARG B:31 , TRP B:32 , LEU B:33 , ASN D:326 , VAL D:327 , TRP D:436
BINDING SITE FOR RESIDUE SCN B 105
17
CC6
SOFTWARE
THR B:73 , ARG D:405 , HOH D:792
BINDING SITE FOR RESIDUE SO4 D 7
18
CC7
SOFTWARE
GLN B:91 , HIS B:95 , HOH B:634 , ARG D:239 , GLU D:242
BINDING SITE FOR RESIDUE SCN B 106
19
CC9
SOFTWARE
MET B:87 , GLY B:90 , GLN B:91 , ASP B:94 , ASP B:98 , PHE B:99 , THR B:100 , HOH B:589 , HOH B:634 , HOH B:636 , ARG D:239 , GLU D:242 , MET D:243 , THR D:329 , PHE D:332 , ARG D:333 , GLY D:335 , HIS D:336 , PHE D:365 , PHE D:407 , LEU D:417 , ARG D:424
BINDING SITE FOR RESIDUE HEM B 107
20
DC4
SOFTWARE
ARG D:161 , HOH D:668
BINDING SITE FOR RESIDUE ACY D 14
21
DC5
SOFTWARE
MET D:522 , ARG D:525
BINDING SITE FOR RESIDUE ACY D 13
22
DC6
SOFTWARE
PRO D:303 , ARG D:307 , ARG D:487 , LYS D:488
BINDING SITE FOR RESIDUE ACY D 12
[
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:
Select:
Label:
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_d1dnu_1 (A:,C:)
1b: SCOP_d1dnu_2 (B:,D:)
View:
Select:
Label:
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
d1dnu.1
A:,C:
1b
d1dnu.2
B:,D:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1dnuC00 (C:113-578)
1b: CATH_1dnuD00 (D:113-578)
View:
Select:
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
1dnuC00
C:113-578
1b
1dnuD00
D:113-578
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain B
Chain D
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (216 KB)
Header - Asym.Unit
Biol.Unit 1 (208 KB)
Header - Biol.Unit 1
Biol.Unit 2 (107 KB)
Header - Biol.Unit 2
Biol.Unit 3 (106 KB)
Header - Biol.Unit 3
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
1DNU
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
