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5AB2
Asym. Unit
Info
Asym.Unit (319 KB)
Biol.Unit 1 (161 KB)
Biol.Unit 2 (155 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF AMINOPEPTIDASE ERAP2 WITH LIGAND
Authors
:
A. Mpakali, P. Giastas, E. Saridakis, I. M. Mavridis, E. Stratikos
Date
:
31 Jul 15 (Deposition) - 30 Sep 15 (Release) - 11 Nov 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.73
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,C (1x)
Biol. Unit 2: B,D (1x)
Keywords
:
Aminopeptidase, Erap2, Zinc Ion Binding, Endoplasmic Reticulum, Hydrolase, Metalloprotease, L-Rap, Antigen Presentation
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Mpakali, P. Giastas, N. Mathioudakis, I. M. Mavridis, E. Saridakis E. Stratikos
Structural Basis For Antigenic Peptide Recognition And Processing By Endoplasmic Reticulum (Er) Aminopeptidase 2.
J. Biol. Chem. V. 290 26021 2015
[
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Hetero Components
(4, 37)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
1c: BETA-D-MANNOSE (BMAc)
1d: BETA-D-MANNOSE (BMAd)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
3d: N-ACETYL-D-GLUCOSAMINE (NAGd)
3e: N-ACETYL-D-GLUCOSAMINE (NAGe)
3f: N-ACETYL-D-GLUCOSAMINE (NAGf)
3g: N-ACETYL-D-GLUCOSAMINE (NAGg)
3h: N-ACETYL-D-GLUCOSAMINE (NAGh)
3i: N-ACETYL-D-GLUCOSAMINE (NAGi)
3j: N-ACETYL-D-GLUCOSAMINE (NAGj)
3k: N-ACETYL-D-GLUCOSAMINE (NAGk)
3l: N-ACETYL-D-GLUCOSAMINE (NAGl)
3m: N-ACETYL-D-GLUCOSAMINE (NAGm)
3n: N-ACETYL-D-GLUCOSAMINE (NAGn)
3o: N-ACETYL-D-GLUCOSAMINE (NAGo)
3p: N-ACETYL-D-GLUCOSAMINE (NAGp)
3q: N-ACETYL-D-GLUCOSAMINE (NAGq)
3r: N-ACETYL-D-GLUCOSAMINE (NAGr)
3s: N-ACETYL-D-GLUCOSAMINE (NAGs)
3t: N-ACETYL-D-GLUCOSAMINE (NAGt)
3u: N-ACETYL-D-GLUCOSAMINE (NAGu)
3v: N-ACETYL-D-GLUCOSAMINE (NAGv)
3w: N-ACETYL-D-GLUCOSAMINE (NAGw)
3x: N-ACETYL-D-GLUCOSAMINE (NAGx)
3y: N-ACETYL-D-GLUCOSAMINE (NAGy)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
4
Ligand/Ion
BETA-D-MANNOSE
2
EDO
6
Ligand/Ion
1,2-ETHANEDIOL
3
NAG
25
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
ZN
2
Ligand/Ion
ZINC ION
[
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Sites
(21, 21)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:370 , HIS A:374 , GLU A:393 , GLY C:1 , PRO C:2
BINDING SITE FOR RESIDUE ZN A1119
02
AC2
SOFTWARE
TYR A:313 , HOH A:2039
BINDING SITE FOR RESIDUE EDO A1962
03
AC3
SOFTWARE
LYS A:476
BINDING SITE FOR RESIDUE EDO A1963
04
AC4
SOFTWARE
HIS B:370 , HIS B:374 , GLU B:393 , GLY D:1 , PRO D:2
BINDING SITE FOR RESIDUE ZN B1119
05
AC5
SOFTWARE
MET B:778
BINDING SITE FOR RESIDUE EDO B1962
06
AC6
SOFTWARE
GLN B:776
BINDING SITE FOR RESIDUE EDO B1963
07
AC7
SOFTWARE
HIS A:83 , ASN A:85 , GLU A:227 , LEU A:248 , HOH A:2075 , ARG B:293
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1001 THROUGH BMA A1003 BOUND TO ASN A 85
08
AC8
SOFTWARE
ASN A:103
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1012 THROUGH NAG A1013 BOUND TO ASN A 103
09
AC9
SOFTWARE
ASN A:119 , ASP A:167
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1004 THROUGH NAG A1005 BOUND TO ASN A 119
10
BC1
SOFTWARE
ASN A:219 , THR A:255 , VAL A:257 , LYS A:258 , TYR A:487
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1006 THROUGH BMA A1008 BOUND TO ASN A 219
11
BC2
SOFTWARE
ASN A:294
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1016 THROUGH NAG A1017 BOUND TO ASN A 294
12
BC3
SOFTWARE
ASN A:405 , HOH A:2079
BINDING SITE FOR MONO-SACCHARIDE NAG A1009 BOUND TO ASN A 405
13
BC4
SOFTWARE
ASN A:431 , LYS A:545
BINDING SITE FOR MONO-SACCHARIDE NAG A1018 BOUND TO ASN A 431
14
BC5
SOFTWARE
ASN A:650 , HOH A:2080 , HOH A:2081
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1010 THROUGH NAG A1011 BOUND TO ASN A 650
15
BC6
SOFTWARE
ASN A:714
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1014 THROUGH NAG A1015 BOUND TO ASN A 714
16
BC7
SOFTWARE
HIS A:272 , SER A:273 , ASP A:291 , ARG A:293 , ASN B:85 , SER B:88 , GLU B:227 , LEU B:248 , HOH B:2001 , HOH B:2020
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B1001 THROUGH BMA B1004 BOUND TO ASN B 85
17
BC8
SOFTWARE
ASN B:103
BINDING SITE FOR MONO-SACCHARIDE NAG B1005 BOUND TO ASN B 103
18
BC9
SOFTWARE
ASN B:219 , THR B:255 , LYS B:258
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B1008 THROUGH NAG B1009 BOUND TO ASN B 219
19
CC1
SOFTWARE
ASN B:405 , LYS B:466 , GLU B:471
BINDING SITE FOR MONO-SACCHARIDE NAG B1010 BOUND TO ASN B 405
20
CC2
SOFTWARE
ASN B:431 , LYS B:545
BINDING SITE FOR MONO-SACCHARIDE NAG B1011 BOUND TO ASN B 431
21
CC3
SOFTWARE
ASN B:650
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B1006 THROUGH NAG B1007 BOUND TO ASN B 650
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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Sorry, no Info available
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Exons
(0, 0)
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(0, 0)
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CATH Domains
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Sorry, no Info available
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Pfam Domains
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Sorry, no Info available
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Chain A
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Asymmetric Unit 1
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Example Command
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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)
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Asym.Unit (319 KB)
Header - Asym.Unit
Biol.Unit 1 (161 KB)
Header - Biol.Unit 1
Biol.Unit 2 (155 KB)
Header - Biol.Unit 2
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