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3MDJ
Biol. Unit 3
Info
Asym.Unit (859 KB)
Biol.Unit 1 (288 KB)
Biol.Unit 2 (289 KB)
Biol.Unit 3 (288 KB)
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(1)
Title
:
ER AMINOPEPTIDASE, ERAP1, BOUND TO THE ZINC AMINOPEPTIDASE INHIBITOR, BESTATIN
Authors
:
T. T. Nguyen, L. J. Stern
Date
:
30 Mar 10 (Deposition) - 30 Mar 11 (Release) - 27 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.95
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Keywords
:
Aminopeptidase, Zn Binding Protein, Er, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. T. Nguyen, S. C. Chang, I. Evnouchidou, I. A. York, C. Zikos, K. L. Rock, A. L. Goldberg, E. Stratikos, L. J. Stern
Structural Basis For Antigenic Peptide Precursor Processing By The Endoplasmic Reticulum Aminopeptidase Erap1.
Nat. Struct. Mol. Biol. V. 18 604 2011
[
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Hetero Components
(4, 6)
Info
All Hetero Components
1a: 2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTY... (BESa)
1b: 2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTY... (BESb)
1c: 2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTY... (BESc)
2a: BETA-D-MANNOSE (BMAa)
2b: BETA-D-MANNOSE (BMAb)
3a: ALPHA-D-MANNOSE (MANa)
3b: ALPHA-D-MANNOSE (MANb)
3c: ALPHA-D-MANNOSE (MANc)
3d: ALPHA-D-MANNOSE (MANd)
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)
5c: ZINC ION (ZNc)
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
BMA
1
Ligand/Ion
BETA-D-MANNOSE
3
MAN
2
Ligand/Ion
ALPHA-D-MANNOSE
4
NAG
2
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
5
ZN
-1
Ligand/Ion
ZINC ION
[
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]
Sites
(7, 7)
Info
All Sites
1: BC6 (SOFTWARE)
2: BC7 (SOFTWARE)
3: BC8 (SOFTWARE)
4: BC9 (SOFTWARE)
5: CC1 (SOFTWARE)
6: CC2 (SOFTWARE)
7: CC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
BC6
SOFTWARE
HIS C:353 , HIS C:357 , GLU C:376 , BES C:1001
BINDING SITE FOR RESIDUE ZN C 1000
2
BC7
SOFTWARE
GLU C:183 , SER C:316 , GLY C:317 , ALA C:318 , MET C:319 , GLU C:320 , THR C:350 , HIS C:353 , GLU C:354 , GLU C:376 , GLU C:383 , ZN C:1000
BINDING SITE FOR RESIDUE BES C 1001
3
BC8
SOFTWARE
HIS C:68 , ASN C:70 , GLU C:210 , LEU C:231 , NAG C:5002
BINDING SITE FOR RESIDUE NAG C 5001
4
BC9
SOFTWARE
GLU C:229 , GLY C:230 , NAG C:5001 , BMA C:5003 , MAN C:5005
BINDING SITE FOR RESIDUE NAG C 5002
5
CC1
SOFTWARE
NAG C:5002 , MAN C:5004 , MAN C:5005
BINDING SITE FOR RESIDUE BMA C 5003
6
CC2
SOFTWARE
GLU C:229 , BMA C:5003
BINDING SITE FOR RESIDUE MAN C 5004
7
CC3
SOFTWARE
NAG C:5002 , BMA C:5003
BINDING SITE FOR RESIDUE MAN C 5005
[
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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 (D346D, chain C, )
05: VAR_012782 (M349V, chain C, )
06: VAR_012783 (R528R, chain C, )
07: VAR_046682 (D575G, chain C, )
08: VAR_021555 (D575N, chain C, )
09: VAR_021556 (R725Q, chain C, )
10: VAR_012784 (E730E, 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
D
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
R
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
E
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
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, 12)
Info
All SCOP Domains
1a: SCOP_d3mdja4 (A:615-934)
1b: SCOP_d3mdjb4 (B:615-934)
1c: SCOP_d3mdjc4 (C:615-934)
2a: SCOP_d3mdja3 (A:530-614)
2b: SCOP_d3mdjb3 (B:530-614)
2c: SCOP_d3mdjc3 (C:530-614)
3a: SCOP_d3mdja1 (A:46-254)
3b: SCOP_d3mdjb1 (B:46-254)
3c: SCOP_d3mdjc1 (C:46-254)
4a: SCOP_d3mdja2 (A:255-529)
4b: SCOP_d3mdjb2 (B:255-529)
4c: SCOP_d3mdjc2 (C:255-529)
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)
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Protein Domains
(
)
(
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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
d3mdja4
A:615-934
1b
d3mdjb4
B:615-934
1c
d3mdjc4
C:615-934
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
d3mdja3
A:530-614
2b
d3mdjb3
B:530-614
2c
d3mdjc3
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
d3mdja1
A:46-254
3b
d3mdjb1
B:46-254
3c
d3mdjc1
C:46-254
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
d3mdja2
A:255-529
4b
d3mdjb2
B:255-529
4c
d3mdjc2
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_3mdjC01 (C:53-441)
1b: PFAM_Peptidase_M1_3mdjC02 (C:53-441)
1c: PFAM_Peptidase_M1_3mdjC03 (C:53-441)
2a: PFAM_DUF3358_3mdjC04 (C:597-916)
2b: PFAM_DUF3358_3mdjC05 (C:597-916)
2c: PFAM_DUF3358_3mdjC06 (C:597-916)
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Organisms
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Clan
:
Peptidase_MA
(251)
Family
:
Peptidase_M1
(15)
Homo sapiens (Human)
(6)
1a
Peptidase_M1-3mdjC01
C:53-441
1b
Peptidase_M1-3mdjC02
C:53-441
1c
Peptidase_M1-3mdjC03
C:53-441
Clan
:
no clan defined [family: DUF3358]
(5)
Family
:
DUF3358
(5)
Homo sapiens (Human)
(3)
2a
DUF3358-3mdjC04
C:597-916
2b
DUF3358-3mdjC05
C:597-916
2c
DUF3358-3mdjC06
C:597-916
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