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4JBS
Biol. Unit 2
Info
Asym.Unit (305 KB)
Biol.Unit 1 (153 KB)
Biol.Unit 2 (148 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE HUMAN ENDOPLASMIC RETICULUM AMINOPEPTIDASE 2 IN COMPLEX WITH PHOSPHINIC PSEUDOTRIPEPTIDE INHIBITOR.
Authors
:
E. Saridakis, J. Birtley, E. Stratikos, I. M. Mavridis
Date
:
20 Feb 13 (Deposition) - 11 Dec 13 (Release) - 25 Dec 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.79
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Thermolysin-Like Catalytic Domain, Hydrolase, Aminopeptidase, Zinc Binding, Endoplasmic Reticulum, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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)
Reference
:
E. Zervoudi, E. Saridakis, J. R. Birtley, S. S. Seregin, E. Reeves, P. Kokkala, Y. A. Aldhamen, A. Amalfitano, I. M. Mavridis, E. James, D. Georgiadis, E. Stratikos
Rationally Designed Inhibitor Targeting Antigen-Trimming Aminopeptidases Enhances Antigen Presentation And Cytotoxic T-Cell Responses.
Proc. Natl. Acad. Sci. Usa V. 110 19890 2013
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Hetero Components
(3, 9)
Info
All Hetero Components
1a: IMIDAZOLE (IMDa)
1b: IMIDAZOLE (IMDb)
2a: ALPHA-D-MANNOSE (MANa)
2b: ALPHA-D-MANNOSE (MANb)
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)
4a: NALPHA-[(2S)-2-{[[(1R)-1-AMINO-3-P... (P52a)
4b: NALPHA-[(2S)-2-{[[(1R)-1-AMINO-3-P... (P52b)
5a: ZINC ION (ZNa)
5b: ZINC ION (ZNb)
View:
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Label:
No.
Name
Count
Type
Full Name
1
IMD
-1
Ligand/Ion
IMIDAZOLE
2
MAN
2
Ligand/Ion
ALPHA-D-MANNOSE
3
NAG
6
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
P52
1
Ligand/Ion
NALPHA-[(2S)-2-{[[(1R)-1-AMINO-3-PHENYLPROPYL](HYDROXY)PHOSPHORYL]METHYL}-4-METHYLPENTANOYL]-L-TRYPTOPHANAMIDE
5
ZN
-1
Ligand/Ion
ZINC ION
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Sites
(10, 10)
Info
All Sites
01: AC9 (SOFTWARE)
02: BC1 (SOFTWARE)
03: BC2 (SOFTWARE)
04: BC3 (SOFTWARE)
05: BC7 (SOFTWARE)
06: BC8 (SOFTWARE)
07: BC9 (SOFTWARE)
08: CC1 (SOFTWARE)
09: CC2 (SOFTWARE)
10: CC3 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC9
SOFTWARE
ARG A:293 , MAN B:1002 , NAG B:1004 , HOH B:1175
BINDING SITE FOR RESIDUE MAN B 1001
02
BC1
SOFTWARE
MAN B:1001
BINDING SITE FOR RESIDUE MAN B 1002
03
BC2
SOFTWARE
HIS B:83 , PRO B:84 , ASN B:85 , GLU B:227 , LEU B:248 , NAG B:1004 , HOH B:1116
BINDING SITE FOR RESIDUE NAG B 1003
04
BC3
SOFTWARE
HIS A:272 , ASP A:291 , GLY B:246 , MAN B:1001 , NAG B:1003
BINDING SITE FOR RESIDUE NAG B 1004
05
BC7
SOFTWARE
ASN B:219 , VAL B:257 , LYS B:258 , TYR B:487 , NAG B:1006 , HOH B:1173
BINDING SITE FOR RESIDUE NAG B 1005
06
BC8
SOFTWARE
NAG B:1005
BINDING SITE FOR RESIDUE NAG B 1006
07
BC9
SOFTWARE
ASN B:431 , HOH B:1165
BINDING SITE FOR RESIDUE NAG B 1007
08
CC1
SOFTWARE
ASN B:294
BINDING SITE FOR RESIDUE NAG B 1008
09
CC2
SOFTWARE
HIS B:370 , HIS B:374 , GLU B:393 , P52 B:1010
BINDING SITE FOR RESIDUE ZN B 1009
10
CC3
SOFTWARE
GLU B:200 , ALA B:335 , GLU B:337 , HIS B:370 , GLU B:371 , LYS B:392 , GLU B:393 , PHE B:450 , TYR B:455 , TYR B:892 , ZN B:1009 , HOH B:1141 , HOH B:1146
BINDING SITE FOR RESIDUE P52 B 1010
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(, 0)
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Exons
(0, 0)
Info
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All Exon Boundaries
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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
(4, 8)
Info
All SCOP Domains
1a: SCOP_d4jbsa4 (A:638-961)
1b: SCOP_d4jbsb4 (B:638-961)
2a: SCOP_d4jbsa3 (A:547-637)
2b: SCOP_d4jbsb3 (B:547-637)
3a: SCOP_d4jbsa1 (A:54-271)
3b: SCOP_d4jbsb1 (B:55-271)
4a: SCOP_d4jbsa2 (A:272-546)
4b: SCOP_d4jbsb2 (B:272-546)
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Classes
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)
(
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(
)
(
)
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(
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
alpha-alpha superhelix
(690)
Superfamily
:
ARM repeat
(317)
Family
:
automated matches
(39)
Protein domain
:
automated matches
(39)
Human (Homo sapiens) [TaxId: 9606]
(21)
1a
d4jbsa4
A:638-961
1b
d4jbsb4
B:638-961
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Zn aminopeptidase insert domain
(10)
Family
:
automated matches
(6)
Protein domain
:
automated matches
(6)
Human (Homo sapiens) [TaxId: 9606]
(5)
2a
d4jbsa3
A:547-637
2b
d4jbsb3
B:547-637
Fold
:
Zn aminopeptidase N-terminal domain
(55)
Superfamily
:
Zn aminopeptidase N-terminal domain
(55)
Family
:
automated matches
(6)
Protein domain
:
automated matches
(6)
Human (Homo sapiens) [TaxId: 9606]
(4)
3a
d4jbsa1
A:54-271
3b
d4jbsb1
B:55-271
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Zincin-like
(701)
Superfamily
:
Metalloproteases (zincins), catalytic domain
(647)
Family
:
automated matches
(37)
Protein domain
:
automated matches
(37)
Human (Homo sapiens) [TaxId: 9606]
(22)
4a
d4jbsa2
A:272-546
4b
d4jbsb2
B:272-546
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CATH Domains
(0, 0)
Info
all CATH domains
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Pfam Domains
(0, 0)
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Sorry, no Info available
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Protein & NOT Site
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Chain B
Asymmetric Unit 1
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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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set fontsize 20
set label size to 20 (allowed range: 1-58)
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Asym.Unit (305 KB)
Header - Asym.Unit
Biol.Unit 1 (153 KB)
Header - Biol.Unit 1
Biol.Unit 2 (148 KB)
Header - Biol.Unit 2
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