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5AB0
Biol. Unit 1
Info
Asym.Unit (329 KB)
Biol.Unit 1 (165 KB)
Biol.Unit 2 (159 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF AMINOPEPTIDASE ERAP2 WITH LIGAND
Authors
:
A. Mpakali, P. Giastas, E. Saridakis, E. Stratikos
Date
:
31 Jul 15 (Deposition) - 30 Sep 15 (Release) - 11 Nov 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,C,E,F
Biol. Unit 1: A,E (1x)
Biol. Unit 2: C,F (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
(7, 20)
Info
All Hetero Components
1a: [(1R)-1-AMINO-3-PHENYLPROPYL]PHOSP... (2X0a)
1b: [(1R)-1-AMINO-3-PHENYLPROPYL]PHOSP... (2X0b)
2a: 2,4-DIMETHYLPENTANAL (7GAa)
2b: 2,4-DIMETHYLPENTANAL (7GAb)
3a: BETA-D-MANNOSE (BMAa)
3b: BETA-D-MANNOSE (BMAb)
3c: BETA-D-MANNOSE (BMAc)
3d: BETA-D-MANNOSE (BMAd)
3e: BETA-D-MANNOSE (BMAe)
4a: 1,2-ETHANEDIOL (EDOa)
4b: 1,2-ETHANEDIOL (EDOb)
4c: 1,2-ETHANEDIOL (EDOc)
4d: 1,2-ETHANEDIOL (EDOd)
5a: 2,6-DIAMINO-HEXANOIC ACID AMIDE (LYNa)
5b: 2,6-DIAMINO-HEXANOIC ACID AMIDE (LYNb)
6a: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESa)
7a: N-ACETYL-D-GLUCOSAMINE (NAGa)
7b: N-ACETYL-D-GLUCOSAMINE (NAGb)
7c: N-ACETYL-D-GLUCOSAMINE (NAGc)
7d: N-ACETYL-D-GLUCOSAMINE (NAGd)
7e: N-ACETYL-D-GLUCOSAMINE (NAGe)
7f: N-ACETYL-D-GLUCOSAMINE (NAGf)
7g: N-ACETYL-D-GLUCOSAMINE (NAGg)
7h: N-ACETYL-D-GLUCOSAMINE (NAGh)
7i: N-ACETYL-D-GLUCOSAMINE (NAGi)
7j: N-ACETYL-D-GLUCOSAMINE (NAGj)
7k: N-ACETYL-D-GLUCOSAMINE (NAGk)
7l: N-ACETYL-D-GLUCOSAMINE (NAGl)
7m: N-ACETYL-D-GLUCOSAMINE (NAGm)
7n: N-ACETYL-D-GLUCOSAMINE (NAGn)
7o: N-ACETYL-D-GLUCOSAMINE (NAGo)
7p: N-ACETYL-D-GLUCOSAMINE (NAGp)
7q: N-ACETYL-D-GLUCOSAMINE (NAGq)
7r: N-ACETYL-D-GLUCOSAMINE (NAGr)
7s: N-ACETYL-D-GLUCOSAMINE (NAGs)
7t: N-ACETYL-D-GLUCOSAMINE (NAGt)
7u: N-ACETYL-D-GLUCOSAMINE (NAGu)
7v: N-ACETYL-D-GLUCOSAMINE (NAGv)
8a: ZINC ION (ZNa)
8b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
2X0
1
Mod. Amino Acid
[(1R)-1-AMINO-3-PHENYLPROPYL]PHOSPHONIC ACID
2
7GA
1
Mod. Amino Acid
2,4-DIMETHYLPENTANAL
3
BMA
2
Ligand/Ion
BETA-D-MANNOSE
4
EDO
2
Ligand/Ion
1,2-ETHANEDIOL
5
LYN
1
Mod. Amino Acid
2,6-DIAMINO-HEXANOIC ACID AMIDE
6
MES
1
Ligand/Ion
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
7
NAG
12
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
8
ZN
-1
Ligand/Ion
ZINC ION
[
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]
Sites
(13, 13)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC8 (SOFTWARE)
06: AC9 (SOFTWARE)
07: BC1 (SOFTWARE)
08: BC2 (SOFTWARE)
09: BC3 (SOFTWARE)
10: BC4 (SOFTWARE)
11: BC5 (SOFTWARE)
12: BC6 (SOFTWARE)
13: BC7 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:370 , HIS A:374 , GLU A:393 , 2X0 E:1
BINDING SITE FOR RESIDUE ZN A1008
02
AC2
SOFTWARE
HIS A:77 , ASP A:79 , SER A:221
BINDING SITE FOR RESIDUE EDO A1964
03
AC3
SOFTWARE
LYS A:283 , SER A:285 , TYR A:287
BINDING SITE FOR RESIDUE EDO A1965
04
AC4
SOFTWARE
NAG A:1074 , BMA A:1075 , HOH A:3276 , HOH A:3277
BINDING SITE FOR RESIDUE MES A2002
05
AC8
SOFTWARE
HIS A:83 , ASN A:85 , GLU A:227 , GLY A:246 , LEU A:248 , ASP C:291
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1071 THROUGH NAG A1072 BOUND TO ASN A 85
06
AC9
SOFTWARE
SER A:102 , ASN A:103 , HOH A:3269 , HOH A:3270
BINDING SITE FOR MONO-SACCHARIDE NAG A1069 BOUND TO ASN A 103
07
BC1
SOFTWARE
THR A:118 , ASN A:119
BINDING SITE FOR MONO-SACCHARIDE NAG A1081 BOUND TO ASN A 119
08
BC2
SOFTWARE
ASN A:219 , THR A:255 , VAL A:257 , LYS A:258 , TYR A:487 , MES A:2002 , HOH A:3271 , HOH A:3275
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1073 THROUGH BMA A1075 BOUND TO ASN A 219
09
BC3
SOFTWARE
ASN A:405 , ASP A:414
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1076 THROUGH BMA A1078 BOUND TO ASN A 405
10
BC4
SOFTWARE
ASN A:431 , LYS A:545
BINDING SITE FOR MONO-SACCHARIDE NAG A1070 BOUND TO ASN A 431
11
BC5
SOFTWARE
ASN A:650 , LEU A:653 , HOH A:3273
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1079 THROUGH NAG A1080 BOUND TO ASN A 650
12
BC6
SOFTWARE
ASN A:714 , HOH A:3274
BINDING SITE FOR MONO-SACCHARIDE NAG A1082 BOUND TO ASN A 714
13
BC7
SOFTWARE
HIS A:272 , SER A:273 , LEU A:274 , PRO A:290 , ASP A:291 , ARG A:293 , HOH A:3084 , HIS C:83 , ASN C:85 , GLU C:227 , LEU C:248 , HOH C:3009 , HOH C:3117 , HOH C:3118 , HOH C:3119 , HOH C:3122
BINDING SITE FOR POLY-SACCHARIDE RESIDUES BMA C1001 THROUGH BMA C1005 BOUND TO ASN C 85
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
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Exons
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Note:
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SCOP Domains
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CATH Domains
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Pfam Domains
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Asymmetric Unit 1
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select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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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 (329 KB)
Header - Asym.Unit
Biol.Unit 1 (165 KB)
Header - Biol.Unit 1
Biol.Unit 2 (159 KB)
Header - Biol.Unit 2
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