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.
PLEASE WAIT...
Getting 'Exon' information from database.
4E36
Asym. Unit
Info
Asym.Unit (302 KB)
Biol.Unit 1 (150 KB)
Biol.Unit 2 (149 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 THE HUMAN ENDOPLASMIC RETICULUM AMINOPEPTIDASE 2 VARIANT N392K
Authors
:
J. R. Birtley, E. Saridakis, P. Pegias, E. Stratikos, I. M. Mavridis
Date
:
09 Mar 12 (Deposition) - 29 Aug 12 (Release) - 17 Oct 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.22
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Thermolysin-Like Catalytic Domain, Hydrolase, Aminopeptidase, Zinc Binding, Glycosylation, Endoplasmic Reticulum
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
I. Evnouchidou, J. Birtley, S. Seregin, A. Papakyriakou, E. Zervoudi M. Samiotaki, G. Panayotou, P. Giastas, O. Petrakis, D. Georgiadis, A. Amalfitano, E. Saridakis, I. M. Mavridis, E. Stratikos
A Common Single Nucleotide Polymorphism In Endoplasmic Reticulum Aminopeptidase 2 Induces A Specificity Switch Tha Leads To Altered Antigen Processing.
J. Immunol. V. 189 2383 2012
[
close entry info
]
Hetero Components
(5, 20)
Info
All Hetero Components
1a: LYSINE (LYSa)
1b: LYSINE (LYSb)
2a: ALPHA-D-MANNOSE (MANa)
2b: ALPHA-D-MANNOSE (MANb)
3a: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESa)
3b: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESb)
4a: N-ACETYL-D-GLUCOSAMINE (NAGa)
4b: N-ACETYL-D-GLUCOSAMINE (NAGb)
4c: N-ACETYL-D-GLUCOSAMINE (NAGc)
4d: N-ACETYL-D-GLUCOSAMINE (NAGd)
4e: N-ACETYL-D-GLUCOSAMINE (NAGe)
4f: N-ACETYL-D-GLUCOSAMINE (NAGf)
4g: N-ACETYL-D-GLUCOSAMINE (NAGg)
4h: N-ACETYL-D-GLUCOSAMINE (NAGh)
4i: N-ACETYL-D-GLUCOSAMINE (NAGi)
4j: N-ACETYL-D-GLUCOSAMINE (NAGj)
4k: N-ACETYL-D-GLUCOSAMINE (NAGk)
4l: N-ACETYL-D-GLUCOSAMINE (NAGl)
5a: ZINC ION (ZNa)
5b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
LYS
2
Mod. Amino Acid
LYSINE
2
MAN
2
Ligand/Ion
ALPHA-D-MANNOSE
3
MES
2
Ligand/Ion
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4
NAG
12
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
5
ZN
2
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(20, 20)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:198 , GLU A:200 , PRO A:333 , ALA A:335 , GLU A:337 , HIS A:370 , GLU A:371 , HIS A:374 , GLU A:393 , TYR A:455 , MES A:1009 , ZN A:1010 , HOH A:1136
BINDING SITE FOR RESIDUE LYS A 1001
02
AC2
SOFTWARE
HIS A:83 , PRO A:84 , ASN A:85 , THR A:87 , ARG A:226 , GLU A:227 , NAG A:1003
BINDING SITE FOR RESIDUE NAG A 1002
03
AC3
SOFTWARE
NAG A:1002 , HOH A:1150
BINDING SITE FOR RESIDUE NAG A 1003
04
AC4
SOFTWARE
HIS A:77 , ASN A:219 , VAL A:257 , LYS A:258 , TYR A:487 , NAG A:1005
BINDING SITE FOR RESIDUE NAG A 1004
05
AC5
SOFTWARE
NAG A:1004 , HOH A:1158
BINDING SITE FOR RESIDUE NAG A 1005
06
AC6
SOFTWARE
ILE A:402 , ASN A:405 , LYS A:466
BINDING SITE FOR RESIDUE NAG A 1006
07
AC7
SOFTWARE
ASN A:650 , THR A:652 , LEU A:653
BINDING SITE FOR RESIDUE NAG A 1007
08
AC8
SOFTWARE
ASN A:103 , HOH A:1138 , HOH A:1146
BINDING SITE FOR RESIDUE NAG A 1008
09
AC9
SOFTWARE
PRO A:333 , GLY A:334 , TRP A:363 , TYR A:892 , LYS A:1001
BINDING SITE FOR RESIDUE MES A 1009
10
BC1
SOFTWARE
HIS A:370 , HIS A:374 , GLU A:393 , LYS A:1001
BINDING SITE FOR RESIDUE ZN A 1010
11
BC2
SOFTWARE
ARG A:293 , MAN B:1002 , NAG B:1004 , HOH B:1135
BINDING SITE FOR RESIDUE MAN B 1001
12
BC3
SOFTWARE
MAN B:1001
BINDING SITE FOR RESIDUE MAN B 1002
13
BC4
SOFTWARE
HIS B:83 , ASN B:85 , GLU B:227 , NAG B:1004
BINDING SITE FOR RESIDUE NAG B 1003
14
BC5
SOFTWARE
ARG A:293 , MAN B:1001 , NAG B:1003
BINDING SITE FOR RESIDUE NAG B 1004
15
BC6
SOFTWARE
ASP B:198 , GLU B:200 , PRO B:333 , GLU B:337 , HIS B:370 , GLU B:371 , HIS B:374 , LYS B:392 , GLU B:393 , TYR B:455 , ZN B:1006 , MES B:1010 , HOH B:1122
BINDING SITE FOR RESIDUE LYS B 1005
16
BC7
SOFTWARE
HIS B:370 , HIS B:374 , GLU B:393 , LYS B:1005
BINDING SITE FOR RESIDUE ZN B 1006
17
BC8
SOFTWARE
HIS B:77 , ASN B:219 , VAL B:257 , LYS B:258 , NAG B:1008
BINDING SITE FOR RESIDUE NAG B 1007
18
BC9
SOFTWARE
NAG B:1007
BINDING SITE FOR RESIDUE NAG B 1008
19
CC1
SOFTWARE
ASN B:431
BINDING SITE FOR RESIDUE NAG B 1009
20
CC2
SOFTWARE
PRO B:333 , GLY B:334 , ASP B:451 , GLU B:452 , TYR B:455 , TYR B:892 , LYS B:1005
BINDING SITE FOR RESIDUE MES B 1010
[
close Site info
]
SAPs(SNPs)/Variants
(4, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_038285 (P214L, chain A/B, )
2: VAR_038286 (K392N, chain A/B, )
3: VAR_051569 (L411R, chain A/B, )
4: VAR_038287 (L669Q, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_038285
P
214
L
ERAP2_HUMAN
Polymorphism
3733905
A/B
P
214
L
2
UniProt
VAR_038286
K
392
N
ERAP2_HUMAN
Polymorphism
2549782
A/B
K
392
N
3
UniProt
VAR_051569
L
411
R
ERAP2_HUMAN
Polymorphism
34261036
A/B
L
411
R
4
UniProt
VAR_038287
L
669
Q
ERAP2_HUMAN
Polymorphism
17408150
A/B
L
669
Q
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: ZINC_PROTEASE (A:367-376,B:367-376)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ZINC_PROTEASE
PS00142
Neutral zinc metallopeptidases, zinc-binding region signature.
ERAP2_HUMAN
367-376
2
A:367-376
B:367-376
[
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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 (302 KB)
Header - Asym.Unit
Biol.Unit 1 (150 KB)
Header - Biol.Unit 1
Biol.Unit 2 (149 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
4E36
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help