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...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
4BM1
Asym. Unit
Info
Asym.Unit (339 KB)
Biol.Unit 1 (167 KB)
Biol.Unit 2 (168 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 MANGANESE PEROXIDASE 4 FROM PLEUROTUS OSTREATUS - CRYSTAL FORM I
Authors
:
F. J. Medrano, A. Romero
Date
:
05 May 13 (Deposition) - 15 Jan 14 (Release) - 25 Jan 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.10
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Oxidoreductase, Class Ii (Fungal) Peroxidases, Protoporphyrin Ix, Electron T Lignin Peroxidase, Lignin Degradation
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Fernandez-Fueyo, F. J. Ruiz-Duenas, M. J. Martinez, A. Romero, K. E. Hammel, F. J. Medrano, A. T. Martinez
Ligninolytic Peroxidase Genes In The Oyster Mushroom Genome: Heterologous Expression, Molecular Structure, Catalytic And Stability Properties, And Lignin-Degrading Ability.
Biotechnol. Biofuels V. 7 2 2014
[
close entry info
]
Hetero Components
(4, 29)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: CITRIC ACID (CITa)
2b: CITRIC ACID (CITb)
3a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
3b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
4f: SULFATE ION (SO4f)
4g: SULFATE ION (SO4g)
4h: SULFATE ION (SO4h)
4i: SULFATE ION (SO4i)
4j: SULFATE ION (SO4j)
4k: SULFATE ION (SO4k)
4l: SULFATE ION (SO4l)
4m: SULFATE ION (SO4m)
4n: SULFATE ION (SO4n)
4o: SULFATE ION (SO4o)
4p: SULFATE ION (SO4p)
4q: SULFATE ION (SO4q)
4r: SULFATE ION (SO4r)
4s: SULFATE ION (SO4s)
4t: SULFATE ION (SO4t)
4u: SULFATE ION (SO4u)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
4
Ligand/Ion
CALCIUM ION
2
CIT
2
Ligand/Ion
CITRIC ACID
3
HEM
2
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
4
SO4
21
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(29, 29)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:49 , GLY A:67 , ASP A:69 , SER A:71 , HOH A:2119 , HOH A:2133
BINDING SITE FOR RESIDUE CA A 401
02
AC2
SOFTWARE
SER A:177 , ASP A:194 , THR A:196 , ASP A:199 , ASP A:201
BINDING SITE FOR RESIDUE CA A 402
03
AC3
SOFTWARE
HIS A:40 , GLU A:41 , ARG A:44 , PHE A:47 , GLU A:147 , PRO A:148 , LEU A:172 , LEU A:173 , SER A:175 , HIS A:176 , ALA A:179 , ALA A:180 , GLN A:181 , ASP A:182 , THR A:183 , ILE A:184 , PHE A:193 , LEU A:235 , SER A:237 , MET A:269 , HOH A:2093 , HOH A:2094 , HOH A:2377
BINDING SITE FOR RESIDUE HEM A 500
04
AC4
SOFTWARE
ASP B:49 , GLY B:67 , ASP B:69 , SER B:71 , HOH B:2108 , HOH B:2120
BINDING SITE FOR RESIDUE CA B 401
05
AC5
SOFTWARE
SER B:177 , ASP B:194 , THR B:196 , ASP B:199 , ASP B:201
BINDING SITE FOR RESIDUE CA B 402
06
AC6
SOFTWARE
HIS B:40 , GLU B:41 , ARG B:44 , PHE B:47 , GLU B:147 , PRO B:148 , LEU B:172 , LEU B:173 , SER B:175 , HIS B:176 , ALA B:179 , ALA B:180 , GLN B:181 , ASP B:182 , THR B:183 , ILE B:184 , PHE B:193 , LEU B:235 , SER B:237 , MET B:269 , HOH B:2083 , HOH B:2097 , HOH B:2142
BINDING SITE FOR RESIDUE HEM B 500
07
AC7
SOFTWARE
SER A:5 , LYS A:6 , HOH A:2003
BINDING SITE FOR RESIDUE SO4 A1339
08
AC8
SOFTWARE
GLU A:34 , CYS A:35 , HOH A:2081 , HOH A:2293 , HOH A:2401
BINDING SITE FOR RESIDUE SO4 A1340
09
AC9
SOFTWARE
LYS A:62 , PHE A:63 , HOH A:2167 , HOH A:2608
BINDING SITE FOR RESIDUE SO4 A1341
10
BC1
SOFTWARE
GLY A:294 , ARG A:295 , HOH A:2524 , HOH A:2609
BINDING SITE FOR RESIDUE SO4 A1342
11
BC2
SOFTWARE
ARG A:295 , LYS A:297 , GLN A:298 , HOH A:2529 , HOH A:2532
BINDING SITE FOR RESIDUE SO4 A1343
12
BC3
SOFTWARE
ALA A:303 , THR A:328 , PHE A:329 , HOH A:2536 , HOH A:2539 , HOH A:2588
BINDING SITE FOR RESIDUE SO4 A1344
13
BC4
SOFTWARE
LYS A:316 , GLY A:327 , THR A:328 , HOH A:2610 , LYS B:101
BINDING SITE FOR RESIDUE SO4 A1345
14
BC5
SOFTWARE
LYS A:281 , HOH A:2068 , ARG B:321 , PRO B:323 , HOH B:2537
BINDING SITE FOR RESIDUE SO4 B1339
15
BC6
SOFTWARE
ARG A:321 , PRO A:323 , HOH A:2576 , HOH A:2579 , LYS B:281 , HOH B:2058
BINDING SITE FOR RESIDUE SO4 A1346
16
BC7
SOFTWARE
HOH A:2251 , THR B:328 , PHE B:329 , THR B:330 , HOH B:2330 , HOH B:2500 , HOH B:2550
BINDING SITE FOR RESIDUE SO4 B1340
17
BC8
SOFTWARE
ASP B:325 , LYS B:326 , HOH B:2540
BINDING SITE FOR RESIDUE SO4 B1341
18
BC9
SOFTWARE
ALA B:303 , THR B:328 , PHE B:329 , HOH B:2501 , HOH B:2506 , HOH B:2547
BINDING SITE FOR RESIDUE SO4 B1342
19
CC1
SOFTWARE
ASN A:12 , ILE A:283 , ASP A:284 , HOH A:2029 , HOH A:2031 , HOH A:2509
BINDING SITE FOR RESIDUE SO4 A1347
20
CC2
SOFTWARE
ASN B:12 , ILE B:283 , ASP B:284 , HOH B:2024 , HOH B:2476 , HOH B:2571
BINDING SITE FOR RESIDUE SO4 B1343
21
CC3
SOFTWARE
ARG B:126 , GLU B:287 , HOH B:2480 , HOH B:2482
BINDING SITE FOR RESIDUE SO4 B1344
22
CC4
SOFTWARE
LYS A:101 , LYS B:316 , GLY B:327 , THR B:328 , HOH B:2429 , HOH B:2572 , HOH B:2573 , HOH B:2574
BINDING SITE FOR RESIDUE SO4 B1345
23
CC5
SOFTWARE
ASP A:325 , LYS A:326 , HOH A:2580 , HOH A:2614
BINDING SITE FOR RESIDUE SO4 A1348
24
CC6
SOFTWARE
LYS B:62 , PHE B:63 , HOH B:2153 , HOH B:2576
BINDING SITE FOR RESIDUE SO4 B1346
25
CC7
SOFTWARE
ARG B:126 , HOH B:2450 , HOH B:2577 , HOH B:2578
BINDING SITE FOR RESIDUE SO4 B1347
26
CC8
SOFTWARE
GLY B:294 , ARG B:295 , HOH B:2490 , HOH B:2579
BINDING SITE FOR RESIDUE SO4 B1348
27
CC9
SOFTWARE
ARG B:295 , LYS B:297 , GLN B:298 , HOH B:2492 , HOH B:2497
BINDING SITE FOR RESIDUE SO4 B1349
28
DC1
SOFTWARE
ILE B:215 , PRO B:216 , PRO B:230 , GLY B:231 , HOH B:2354 , HOH B:2386 , HOH B:2402 , HOH B:2404 , HOH B:2580 , HOH B:2581 , HOH B:2582
BINDING SITE FOR RESIDUE CIT B1350
29
DC2
SOFTWARE
ILE A:215 , PRO A:216 , PRO A:230 , GLY A:231 , HOH A:2389 , HOH A:2422 , HOH A:2439 , HOH A:2441 , HOH A:2615 , HOH A:2616 , HOH A:2617 , HOH A:2618
BINDING SITE FOR RESIDUE CIT A1349
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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.
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d4bm1a_ (A:)
1b: SCOP_d4bm1b_ (B:)
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
:
automated matches
(40)
Protein domain
:
automated matches
(40)
Oyster mushroom (Pleurotus ostreatus) [TaxId: 5322]
(11)
1a
d4bm1a_
A:
1b
d4bm1b_
B:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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
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 (339 KB)
Header - Asym.Unit
Biol.Unit 1 (167 KB)
Header - Biol.Unit 1
Biol.Unit 2 (168 KB)
Header - Biol.Unit 2
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
4BM1
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help