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3SE6
Biol. Unit 1
Info
Asym.Unit (300 KB)
Biol.Unit 1 (150 KB)
Biol.Unit 2 (148 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE HUMAN ENDOPLASMIC RETICULUM AMINOPEPTIDASE 2
Authors
:
J. R. Birtley, E. Saridakis, E Stratikos, I. M. Mavridis
Date
:
10 Jun 11 (Deposition) - 21 Dec 11 (Release) - 21 Mar 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.08
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Thermolysin-Like Catalytic Domain, Aminopeptidase, Zinc Binding, Glycosylation, Endoplasmic Reticulum, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. R. Birtley, E. Saridakis, E. Stratikos, I. M. Mavridis
The Crystal Structure Of Human Endoplasmic Reticulum Aminopeptidase 2 Reveals The Atomic Basis For Distinct Role In Antigen Processing.
Biochemistry V. 51 286 2012
[
close entry info
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Hetero Components
(3, 8)
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)
5a: ZINC ION (ZNa)
5b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
LYS
1
Mod. Amino Acid
LYSINE
2
MAN
-1
Ligand/Ion
ALPHA-D-MANNOSE
3
MES
1
Ligand/Ion
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4
NAG
6
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
5
ZN
-1
Ligand/Ion
ZINC ION
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Sites
(11, 11)
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: BC3 (SOFTWARE)
11: BC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:370 , HIS A:374 , GLU A:393 , LYS A:968
BINDING SITE FOR RESIDUE ZN A 5000
02
AC2
SOFTWARE
ASP A:198 , GLU A:200 , PRO A:333 , ALA A:335 , MET A:336 , GLU A:337 , HIS A:370 , GLU A:371 , HIS A:374 , GLU A:393 , TYR A:455 , MES A:1083 , ZN A:5000
BINDING SITE FOR RESIDUE LYS A 968
03
AC3
SOFTWARE
HIS A:83 , ASN A:85 , ARG A:226 , GLU A:227 , LEU A:248 , NAG A:1072
BINDING SITE FOR RESIDUE NAG A 1071
04
AC4
SOFTWARE
HOH A:1042 , NAG A:1071
BINDING SITE FOR RESIDUE NAG A 1072
05
AC5
SOFTWARE
ASN A:219 , VAL A:257 , LYS A:258 , TYR A:487 , NAG A:1074
BINDING SITE FOR RESIDUE NAG A 1073
06
AC6
SOFTWARE
NAG A:1073
BINDING SITE FOR RESIDUE NAG A 1074
07
AC7
SOFTWARE
ASN A:405 , LYS A:466
BINDING SITE FOR RESIDUE NAG A 1075
08
AC8
SOFTWARE
ASN A:650
BINDING SITE FOR RESIDUE NAG A 1076
09
AC9
SOFTWARE
PRO A:333 , GLY A:334 , PHE A:450 , ASP A:451 , GLU A:452 , TYR A:892 , LYS A:968
BINDING SITE FOR RESIDUE MES A 1083
10
BC3
SOFTWARE
ARG A:293 , NAG B:1078 , MAN B:1080
BINDING SITE FOR RESIDUE MAN B 1079
11
BC6
SOFTWARE
HIS A:272 , ARG A:293 , NAG B:1077 , MAN B:1079
BINDING SITE FOR RESIDUE NAG B 1078
[
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SAPs(SNPs)/Variants
(4, 4)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_038285 (P214L, chain A, )
2: VAR_038286 (N392N, chain A, )
3: VAR_051569 (L411R, chain A, )
4: VAR_038287 (L669Q, chain A, )
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
P
214
L
2
UniProt
VAR_038286
K
392
N
ERAP2_HUMAN
Polymorphism
2549782
A
N
392
N
3
UniProt
VAR_051569
L
411
R
ERAP2_HUMAN
Polymorphism
34261036
A
L
411
R
4
UniProt
VAR_038287
L
669
Q
ERAP2_HUMAN
Polymorphism
17408150
A
L
669
Q
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: ZINC_PROTEASE (A: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
1
A:367-376
-
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Exons
(0, 0)
Info
All Exons
View:
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(4, 8)
Info
All SCOP Domains
1a: SCOP_d3se6a4 (A:638-961)
1b: SCOP_d3se6b4 (B:638-961)
2a: SCOP_d3se6a3 (A:547-637)
2b: SCOP_d3se6b3 (B:547-637)
3a: SCOP_d3se6a1 (A:54-271)
3b: SCOP_d3se6b1 (B:55-271)
4a: SCOP_d3se6a2 (A:272-546)
4b: SCOP_d3se6b2 (B:272-546)
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Protein Domains
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(
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Organisms
(
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(
)
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
d3se6a4
A:638-961
1b
d3se6b4
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
d3se6a3
A:547-637
2b
d3se6b3
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
d3se6a1
A:54-271
3b
d3se6b1
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
d3se6a2
A:272-546
4b
d3se6b2
B:272-546
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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All Atoms
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Protein & NOT Site
Protein & NOT PROSITE
Chain A
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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select non-helix/non-sheet protein parts
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Asym.Unit (300 KB)
Header - Asym.Unit
Biol.Unit 1 (150 KB)
Header - Biol.Unit 1
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