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3QNF
Asym. Unit
Info
Asym.Unit (374 KB)
Biol.Unit 1 (113 KB)
Biol.Unit 2 (131 KB)
Biol.Unit 3 (129 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE OPEN STATE OF HUMAN ENDOPLASMIC RETICULUM AMINOPEPTIDASE 1 ERAP1
Authors
:
M. Vollmar, G. Kochan, T. Krojer, D. Harvey, A. Chaikuad, C. Allerston, J. R. C. Muniz, J. Raynor, E. Ugochukwu, G. Berridge, B. P. Wordsworth, Delft, C. Bountra, C. H. Arrowsmith, A. Edwards, K. Kavanagh, U. Opper Structural Genomics Consortium (Sgc)
Date
:
08 Feb 11 (Deposition) - 23 Feb 11 (Release) - 25 May 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Keywords
:
Structural Genomics Consortium, Sgc, Glycoprotein, Metal-Binding, Metalloprotease, Protease, Adaptive Immunity, Hydrolase
(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
(3, 11)
Info
All Hetero Components
1a: ALPHA-D-MANNOSE (MANa)
1b: ALPHA-D-MANNOSE (MANb)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2b: N-ACETYL-D-GLUCOSAMINE (NAGb)
2c: N-ACETYL-D-GLUCOSAMINE (NAGc)
2d: N-ACETYL-D-GLUCOSAMINE (NAGd)
2e: N-ACETYL-D-GLUCOSAMINE (NAGe)
2f: N-ACETYL-D-GLUCOSAMINE (NAGf)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MAN
2
Ligand/Ion
ALPHA-D-MANNOSE
2
NAG
6
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
3
ZN
3
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: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:320 , HIS A:353 , HIS A:357 , GLU A:376
BINDING SITE FOR RESIDUE ZN A 5000
02
AC2
SOFTWARE
HIS A:68 , ASN A:70 , GLU A:210 , LEU A:231 , NAG A:1002
BINDING SITE FOR RESIDUE NAG A 1001
03
AC3
SOFTWARE
GLU A:229 , GLY A:230 , NAG A:1001 , MAN A:1004
BINDING SITE FOR RESIDUE NAG A 1002
04
AC4
SOFTWARE
GLU A:229 , NAG A:1002 , MAN A:1005 , ALA C:111
BINDING SITE FOR RESIDUE MAN A 1004
05
AC5
SOFTWARE
MAN A:1004 , HIS B:611 , GLU B:613 , GLY B:650 , LYS B:651 , LEU B:652 , ALA C:111
BINDING SITE FOR RESIDUE MAN A 1005
06
AC6
SOFTWARE
HIS B:353 , HIS B:357 , GLU B:376
BINDING SITE FOR RESIDUE ZN B 5000
07
AC7
SOFTWARE
ASN B:154
BINDING SITE FOR RESIDUE NAG B 1154
08
AC8
SOFTWARE
HIS B:68 , ASN B:70 , GLU B:210 , LEU B:231
BINDING SITE FOR RESIDUE NAG B 1070
09
AC9
SOFTWARE
GLU C:320 , HIS C:353 , HIS C:357 , GLU C:376
BINDING SITE FOR RESIDUE ZN C 5000
10
BC1
SOFTWARE
HIS C:68 , ASN C:70 , GLU C:210 , LEU C:231
BINDING SITE FOR RESIDUE NAG C 1070
11
BC2
SOFTWARE
ASN C:154
BINDING SITE FOR RESIDUE NAG C 1154
[
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SAPs(SNPs)/Variants
(10, 30)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_046681 (E56K, chain A/B/C, )
02: VAR_012779 (R127P, chain A/B/C, )
03: VAR_012780 (I276M, chain A/B/C, )
04: VAR_012781 (G346D, chain A/B/C, )
05: VAR_012782 (M349V, chain A/B/C, )
06: VAR_012783 (K528R, chain A/B/C, )
07: VAR_046682 (D575G, chain A/B/C, )
08: VAR_021555 (D575N, chain A/B/C, )
09: VAR_021556 (R725Q, chain A/B/C, )
10: VAR_012784 (Q730E, chain A/B/C, )
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/B/C
E
56
K
02
UniProt
VAR_012779
R
127
P
ERAP1_HUMAN
Polymorphism
26653
A/B/C
R
127
P
03
UniProt
VAR_012780
I
276
M
ERAP1_HUMAN
Polymorphism
26618
A/B/C
I
276
M
04
UniProt
VAR_012781
G
346
D
ERAP1_HUMAN
Polymorphism
27895
A/B/C
G
346
D
05
UniProt
VAR_012782
M
349
V
ERAP1_HUMAN
Polymorphism
2287987
A/B/C
M
349
V
06
UniProt
VAR_012783
K
528
R
ERAP1_HUMAN
Polymorphism
30187
A/B/C
K
528
R
07
UniProt
VAR_046682
D
575
G
ERAP1_HUMAN
Polymorphism
6863093
A/B/C
D
575
G
08
UniProt
VAR_021555
D
575
N
ERAP1_HUMAN
Polymorphism
10050860
A/B/C
D
575
N
09
UniProt
VAR_021556
R
725
Q
ERAP1_HUMAN
Polymorphism
17482078
A/B/C
R
725
Q
10
UniProt
VAR_012784
Q
730
E
ERAP1_HUMAN
Polymorphism
27044
A/B/C
Q
730
E
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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PROSITE Patterns/Profiles
(1, 3)
Info
All PROSITE Patterns/Profiles
1: ZINC_PROTEASE (A:350-359,B:350-359,C: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
3
A:350-359
B:350-359
C:350-359
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Exons
(0, 0)
Info
All Exons
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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.
SCOP Domains
(4, 11)
Info
All SCOP Domains
1a: SCOP_d3qnfb4 (B:615-935)
1b: SCOP_d3qnfc4 (C:615-937)
2a: SCOP_d3qnfa3 (A:530-614)
2b: SCOP_d3qnfb3 (B:530-614)
2c: SCOP_d3qnfc3 (C:530-614)
3a: SCOP_d3qnfa1 (A:46-254)
3b: SCOP_d3qnfb1 (B:46-254)
3c: SCOP_d3qnfc1 (C:47-254)
4a: SCOP_d3qnfa2 (A:255-529)
4b: SCOP_d3qnfb2 (B:255-529)
4c: SCOP_d3qnfc2 (C:255-529)
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Classes
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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
d3qnfb4
B:615-935
1b
d3qnfc4
C:615-937
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
d3qnfa3
A:530-614
2b
d3qnfb3
B:530-614
2c
d3qnfc3
C:530-614
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
d3qnfa1
A:46-254
3b
d3qnfb1
B:46-254
3c
d3qnfc1
C:47-254
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
d3qnfa2
A:255-529
4b
d3qnfb2
B:255-529
4c
d3qnfc2
C:255-529
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CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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Pfam Domains
(2, 6)
Info
all PFAM domains
1a: PFAM_Peptidase_M1_3qnfC01 (C:53-441)
1b: PFAM_Peptidase_M1_3qnfC02 (C:53-441)
1c: PFAM_Peptidase_M1_3qnfC03 (C:53-441)
2a: PFAM_DUF3358_3qnfC04 (C:597-916)
2b: PFAM_DUF3358_3qnfC05 (C:597-916)
2c: PFAM_DUF3358_3qnfC06 (C:597-916)
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Clans
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Organisms
(
)
(
)
Clan
:
Peptidase_MA
(251)
Family
:
Peptidase_M1
(15)
Homo sapiens (Human)
(6)
1a
Peptidase_M1-3qnfC01
C:53-441
1b
Peptidase_M1-3qnfC02
C:53-441
1c
Peptidase_M1-3qnfC03
C:53-441
Clan
:
no clan defined [family: DUF3358]
(5)
Family
:
DUF3358
(5)
Homo sapiens (Human)
(3)
2a
DUF3358-3qnfC04
C:597-916
2b
DUF3358-3qnfC05
C:597-916
2c
DUF3358-3qnfC06
C:597-916
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