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.
1D5L
Biol. Unit 1
Info
Asym.Unit (217 KB)
Biol.Unit 1 (209 KB)
Biol.Unit 2 (108 KB)
Biol.Unit 3 (108 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
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
]
Hetero Components
(9, 34)
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
7
Ligand/Ion
ACETATE ION
2
BMA
2
Ligand/Ion
BETA-D-MANNOSE
3
CA
-1
Ligand/Ion
CALCIUM ION
4
CL
-1
Ligand/Ion
CHLORIDE ION
5
CSO
2
Mod. Amino Acid
S-HYDROXYCYSTEINE
6
CYN
4
Ligand/Ion
CYANIDE ION
7
FUC
2
Ligand/Ion
ALPHA-L-FUCOSE
8
HEM
2
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
9
MAN
4
Ligand/Ion
ALPHA-D-MANNOSE
10
NAG
8
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
11
SO4
3
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(35, 35)
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: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (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:721A , HOH C:988A , HOH C:989A
BINDING SITE FOR RESIDUE NAG C 1620
02
AC2
SOFTWARE
ASN C:225 , ALA C:228 , LEU C:373
BINDING SITE FOR RESIDUE NAG C 1630
03
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
04
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
05
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
06
AC6
SOFTWARE
BMA C:1642 , LYS D:308
BINDING SITE FOR RESIDUE MAN C 1643
07
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
08
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
09
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
10
BC1
SOFTWARE
ASN D:225 , ALA D:228 , TRP D:369
BINDING SITE FOR RESIDUE NAG D 2630
11
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
12
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
13
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
14
BC5
SOFTWARE
LYS C:308 , BMA D:2642
BINDING SITE FOR RESIDUE MAN D 2643
15
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
16
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
17
BC8
SOFTWARE
ASP A:96 , THR C:168 , PHE C:170 , ASP C:172 , SER C:174
BINDING SITE FOR RESIDUE CA C 1600
18
BC9
SOFTWARE
ARG A:31 , TRP A:32 , ASN C:326 , VAL C:327 , TRP C:436
BINDING SITE FOR RESIDUE CL A 1601
19
CC1
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
20
CC2
SOFTWARE
ARG C:229 , THR C:447 , GLY C:449 , GLN C:450 , HOH C:960A
BINDING SITE FOR RESIDUE SO4 C 1603
21
CC3
SOFTWARE
PRO C:123 , ARG C:161 , HOH C:661A , HOH C:1213A , HOH C:1281A
BINDING SITE FOR RESIDUE ACT C 1606
22
CC4
SOFTWARE
ARG C:525
BINDING SITE FOR RESIDUE ACT C 1604
23
CC5
SOFTWARE
PRO C:303 , ARG C:307 , ARG C:487
BINDING SITE FOR RESIDUE ACT C 1607
24
CC6
SOFTWARE
GLN A:91 , HIS A:95 , HEM A:605 , HOH A:843A , HOH A:845A
BINDING SITE FOR RESIDUE CYN A 1844
25
CC7
SOFTWARE
GLN C:201 , PRO C:212 , PHE C:213
BINDING SITE FOR RESIDUE CYN C 1889
26
CC8
SOFTWARE
ASP B:96 , THR D:168 , PHE D:170 , ASP D:172 , SER D:174
BINDING SITE FOR RESIDUE CA D 2600
27
CC9
SOFTWARE
ARG B:31 , TRP B:32 , ASN D:326 , VAL D:327 , TRP D:436
BINDING SITE FOR RESIDUE CL B 2601
28
DC1
SOFTWARE
THR B:73 , HOH B:961B , ARG D:405 , HOH D:842B
BINDING SITE FOR RESIDUE SO4 D 2602
29
DC2
SOFTWARE
PRO D:124 , ARG D:161 , HOH D:661B , HOH D:981B , HOH D:1278B
BINDING SITE FOR RESIDUE ACT D 2606
30
DC3
SOFTWARE
ARG D:525
BINDING SITE FOR RESIDUE ACT D 2604
31
DC4
SOFTWARE
PRO D:303 , ARG D:307 , ARG D:487 , LYS D:488
BINDING SITE FOR RESIDUE ACT D 2607
32
DC5
SOFTWARE
GLN B:91 , HIS B:95 , HEM B:605 , HOH B:843B , HOH B:845B
BINDING SITE FOR RESIDUE CYN B 2844
33
DC6
SOFTWARE
ASN D:200 , GLN D:201 , PHE D:213
BINDING SITE FOR RESIDUE CYN D 2889
34
DC7
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:846A , CYN A:1844 , 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:365 , PHE C:407 , LEU C:417 , ARG C:424
BINDING SITE FOR RESIDUE HEM A 605
35
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, 16)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_015377 (Y7C, chain A/B, )
2: VAR_015378 (M85T, chain A/B, )
3: VAR_036517 (R281Q, chain C/D, )
4: VAR_PERM_HUMAN_CCDS11604_1_01 (R281Q, chain C/D, )
5: VAR_015379 (R403W, chain C/D, )
6: VAR_023996 (R438C, chain C/D, )
7: VAR_023997 (E517Q, chain C/D, )
8: VAR_012066 (I551V, chain C/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
A/B
Y
7
C
2
UniProt
VAR_015378
M
251
T
PERM_HUMAN
Disease (MPOD)
56378716
A/B
M
85
T
3
UniProt
VAR_036517
R
447
Q
PERM_HUMAN
Unclassified
---
C/D
R
281
Q
4
CancerSNP
VAR_PERM_HUMAN_CCDS11604_1_01
*
R
447
Q
PERM_HUMAN
Disease (Colorectal cancer)
---
C/D
R
281
Q
5
UniProt
VAR_015379
R
569
W
PERM_HUMAN
Disease (MPOD)
---
C/D
R
403
W
6
UniProt
VAR_023996
R
604
C
PERM_HUMAN
Polymorphism
35670089
C/D
R
438
C
7
UniProt
VAR_023997
E
683
Q
PERM_HUMAN
Polymorphism
35702888
C/D
E
517
Q
8
UniProt
VAR_012066
I
717
V
PERM_HUMAN
Polymorphism
2759
C/D
I
551
V
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: PEROXIDASE_1 (C:242-252,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
2
C:242-252
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_d1d5l_1 (A:,C:)
1b: SCOP_d1d5l_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
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:
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
1d5lC00
C:113-578
1b
1d5lD00
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 A
Chain B
Chain C
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 (217 KB)
Header - Asym.Unit
Biol.Unit 1 (209 KB)
Header - Biol.Unit 1
Biol.Unit 2 (108 KB)
Header - Biol.Unit 2
Biol.Unit 3 (108 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
1D5L
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help