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3QNF
Biol. Unit 3
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
(1, 2)
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
-1
Ligand/Ion
ALPHA-D-MANNOSE
2
NAG
2
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
3
ZN
-1
Ligand/Ion
ZINC ION
[
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Sites
(5, 5)
Info
All Sites
1: AC4 (SOFTWARE)
2: AC5 (SOFTWARE)
3: AC9 (SOFTWARE)
4: BC1 (SOFTWARE)
5: BC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC4
SOFTWARE
GLU A:229 , NAG A:1002 , MAN A:1005 , ALA C:111
BINDING SITE FOR RESIDUE MAN A 1004
2
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
3
AC9
SOFTWARE
GLU C:320 , HIS C:353 , HIS C:357 , GLU C:376
BINDING SITE FOR RESIDUE ZN C 5000
4
BC1
SOFTWARE
HIS C:68 , ASN C:70 , GLU C:210 , LEU C:231
BINDING SITE FOR RESIDUE NAG C 1070
5
BC2
SOFTWARE
ASN C:154
BINDING SITE FOR RESIDUE NAG C 1154
[
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SAPs(SNPs)/Variants
(10, 10)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_046681 (E56K, chain C, )
02: VAR_012779 (R127P, chain C, )
03: VAR_012780 (I276M, chain C, )
04: VAR_012781 (G346D, chain C, )
05: VAR_012782 (M349V, chain C, )
06: VAR_012783 (K528R, chain C, )
07: VAR_046682 (D575G, chain C, )
08: VAR_021555 (D575N, chain C, )
09: VAR_021556 (R725Q, chain C, )
10: VAR_012784 (Q730E, chain 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
C
E
56
K
02
UniProt
VAR_012779
R
127
P
ERAP1_HUMAN
Polymorphism
26653
C
R
127
P
03
UniProt
VAR_012780
I
276
M
ERAP1_HUMAN
Polymorphism
26618
C
I
276
M
04
UniProt
VAR_012781
G
346
D
ERAP1_HUMAN
Polymorphism
27895
C
G
346
D
05
UniProt
VAR_012782
M
349
V
ERAP1_HUMAN
Polymorphism
2287987
C
M
349
V
06
UniProt
VAR_012783
K
528
R
ERAP1_HUMAN
Polymorphism
30187
C
K
528
R
07
UniProt
VAR_046682
D
575
G
ERAP1_HUMAN
Polymorphism
6863093
C
D
575
G
08
UniProt
VAR_021555
D
575
N
ERAP1_HUMAN
Polymorphism
10050860
C
D
575
N
09
UniProt
VAR_021556
R
725
Q
ERAP1_HUMAN
Polymorphism
17482078
C
R
725
Q
10
UniProt
VAR_012784
Q
730
E
ERAP1_HUMAN
Polymorphism
27044
C
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 (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
1
-
-
C:350-359
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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, 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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Protein Domains
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)
(
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Organisms
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(
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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
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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Asymmetric Unit 1
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