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2YD0
Asym. Unit
Info
Asym.Unit (154 KB)
Biol.Unit 1 (148 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE SOLUBLE DOMAIN OF HUMAN ENDOPLASMIC RETICULUM AMINOPEPTIDASE 1 ERAP1
Authors
:
M. Vollmar, G. Kochan, T. Krojer, E. Ugochukwu, J. R. C. Muniz, J. Raynor A. Chaikuad, C. Allerston, F. Von Delft, C. Bountra, C. H. Arrowsmith J. Weigelt, A. Edwards, S. Knapp
Date
:
17 Mar 11 (Deposition) - 13 Apr 11 (Release) - 03 Oct 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Hydrolase, Glycoprotein, Metal-Binding, Metalloprotease, Protease, Adaptive Immunity
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. Kochan, T. Krojer, D. Harvey, R. Fischer, L. Chen, M. Vollmar, F. Von Delft, K. L. Kavanagh, M. A. Brown, P. Bowness, P. Wordsworth, B. M. Kessler, U. Oppermann
Crystal Structures Of The Endoplasmic Reticulum Aminopeptidase-1 (Erap1) Reveal The Molecular Basis For N-Terminal Peptide Trimming.
Proc. Natl. Acad. Sci. Usa V. 108 7745 2011
[
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Hetero Components
(5, 10)
Info
All Hetero Components
1a: 2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTY... (BESa)
2a: 1,2-ETHANEDIOL (EDOa)
3a: POTASSIUM ION (Ka)
3b: POTASSIUM ION (Kb)
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)
5a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BES
1
Ligand/Ion
2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID
2
EDO
1
Ligand/Ion
1,2-ETHANEDIOL
3
K
2
Ligand/Ion
POTASSIUM ION
4
NAG
5
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
5
ZN
1
Ligand/Ion
ZINC ION
[
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Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:353 , HIS A:357 , GLU A:376 , BES A:1950
BINDING SITE FOR RESIDUE ZN A1946
2
AC2
SOFTWARE
GLU A:431 , ARG A:906
BINDING SITE FOR RESIDUE K A1947
3
AC3
SOFTWARE
ASP A:295 , SER A:298
BINDING SITE FOR RESIDUE K A1948
4
AC4
SOFTWARE
TYR A:451 , ARG A:579
BINDING SITE FOR RESIDUE EDO A1949
5
AC5
SOFTWARE
GLN A:181 , GLU A:183 , SER A:316 , GLY A:317 , ALA A:318 , MET A:319 , GLU A:320 , HIS A:353 , GLU A:354 , HIS A:357 , GLU A:376 , LYS A:380 , TYR A:438 , ZN A:1946
BINDING SITE FOR RESIDUE BES A1950
6
AC6
SOFTWARE
HIS A:68 , ALA A:69 , ASN A:70 , GLN A:88 , HIS A:99 , ASN A:154 , GLU A:210 , GLU A:229 , ASN A:414 , NAG A:1945
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 70 RESIDUES 1941 TO 1944
7
AC7
SOFTWARE
GLN A:88 , HIS A:99 , ASN A:154 , GLU A:229 , ASN A:414 , NAG A:1941
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 154 RESIDUES 1942 TO 1945
[
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SAPs(SNPs)/Variants
(10, 10)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_046681 (E56K, chain A, )
02: VAR_012779 (R127P, chain A, )
03: VAR_012780 (I276M, chain A, )
04: VAR_012781 (G346D, chain A, )
05: VAR_012782 (M349V, chain A, )
06: VAR_012783 (K528R, chain A, )
07: VAR_046682 (D575G, chain A, )
08: VAR_021555 (D575N, chain A, )
09: VAR_021556 (R725Q, chain A, )
10: VAR_012784 (Q730E, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_046681
E
56
K
ERAP1_HUMAN
Polymorphism
3734016
A
E
56
K
02
UniProt
VAR_012779
R
127
P
ERAP1_HUMAN
Polymorphism
26653
A
R
127
P
03
UniProt
VAR_012780
I
276
M
ERAP1_HUMAN
Polymorphism
26618
A
I
276
M
04
UniProt
VAR_012781
G
346
D
ERAP1_HUMAN
Polymorphism
27895
A
G
346
D
05
UniProt
VAR_012782
M
349
V
ERAP1_HUMAN
Polymorphism
2287987
A
M
349
V
06
UniProt
VAR_012783
K
528
R
ERAP1_HUMAN
Polymorphism
30187
A
K
528
R
07
UniProt
VAR_046682
D
575
G
ERAP1_HUMAN
Polymorphism
6863093
A
D
575
G
08
UniProt
VAR_021555
D
575
N
ERAP1_HUMAN
Polymorphism
10050860
A
D
575
N
09
UniProt
VAR_021556
R
725
Q
ERAP1_HUMAN
Polymorphism
17482078
A
R
725
Q
10
UniProt
VAR_012784
Q
730
E
ERAP1_HUMAN
Polymorphism
27044
A
Q
730
E
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:350-359)
;
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.
ERAP1_HUMAN
350-359
1
A:350-359
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Exons
(0, 0)
Info
All Exons
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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.
SCOP Domains
(4, 4)
Info
All SCOP Domains
1a: SCOP_d2yd0a4 (A:615-940)
2a: SCOP_d2yd0a3 (A:530-614)
3a: SCOP_d2yd0a1 (A:46-254)
4a: SCOP_d2yd0a2 (A:255-529)
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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
:
ERAP1 C-terminal-like
(4)
Protein domain
:
ERAP1 C-terminal domain
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d2yd0a4
A:615-940
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Zn aminopeptidase insert domain
(10)
Family
:
Zn aminopeptidase insert domain
(4)
Protein domain
:
ERAP1 insert domain
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
2a
d2yd0a3
A:530-614
Fold
:
Zn aminopeptidase N-terminal domain
(55)
Superfamily
:
Zn aminopeptidase N-terminal domain
(55)
Family
:
Zn aminopeptidase N-terminal domain
(49)
Protein domain
:
ERAP1 N-terminal domain
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
3a
d2yd0a1
A:46-254
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Zincin-like
(701)
Superfamily
:
Metalloproteases (zincins), catalytic domain
(647)
Family
:
Zn aminopeptidase catalytic domain
(49)
Protein domain
:
ERAP1 catalytic domain
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
4a
d2yd0a2
A:255-529
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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
(2, 2)
Info
all PFAM domains
1a: PFAM_Peptidase_M1_2yd0A01 (A:53-441)
2a: PFAM_DUF3358_2yd0A02 (A:597-916)
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Clans
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)
Families
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(
)
Organisms
(
)
(
)
Clan
:
Peptidase_MA
(251)
Family
:
Peptidase_M1
(15)
Homo sapiens (Human)
(6)
1a
Peptidase_M1-2yd0A01
A:53-441
Clan
:
no clan defined [family: DUF3358]
(5)
Family
:
DUF3358
(5)
Homo sapiens (Human)
(3)
2a
DUF3358-2yd0A02
A:597-916
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Chain A
Asymmetric Unit 1
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