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1AVF
Asym. Unit
Info
Asym.Unit (121 KB)
Biol.Unit 1 (60 KB)
Biol.Unit 2 (60 KB)
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(1)
Title
:
ACTIVATION INTERMEDIATE 2 OF HUMAN GASTRICSIN FROM HUMAN STOMACH
Authors
:
A. R. Khan, M. M. Cherney, N. I. Tarasova, M. N. G. James
Date
:
16 Sep 97 (Deposition) - 25 Feb 98 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.36
Chains
:
Asym. Unit : A,J,P,Q
Biol. Unit 1: A,P (1x)
Biol. Unit 2: J,Q (1x)
Keywords
:
Aspartyl Protease, Gastricsin, Aspartic Proteinase, Intermediate, Activation, Acid
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. R. Khan, M. M. Cherney, N. I. Tarasova, M. N. James
Structural Characterization Of Activation 'Intermediate 2' On The Pathway To Human Gastricsin.
Nat. Struct. Biol. V. 4 1010 1997
(for further references see the
PDB file header
)
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: SODIUM ION (NAa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NA
1
Ligand/Ion
SODIUM ION
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Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
SER A:275 , SER A:311 , HOH A:332 , HOH A:335 , HOH A:342 , HOH A:471
BINDING SITE FOR RESIDUE NA A 330
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 6)
Info
All PROSITE Patterns/Profiles
1: PEPTIDASE_A1 (A:14-326,J:14-326)
2: ASP_PROTEASE (A:29-40,J:29-40|A:214-225,J:214-22...)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PEPTIDASE_A1
PS51767
Peptidase family A1 domain profile.
PEPC_HUMAN
73-385
2
A:14-326
J:14-326
2
ASP_PROTEASE
PS00141
Eukaryotic and viral aspartyl proteases active site.
PEPC_HUMAN
88-99
273-284
4
A:29-40
J:29-40
A:214-225
J:214-225
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Exons
(9, 20)
Info
All Exons
Exon 1.2a (- | - | P:1-4 | Q:1-4)
Exon 1.3 (A:2-11 | J:2-11 | P:4-21 | Q:4-22)
Exon 1.4c (A:12-51 | J:12-51 | - | -)
Exon 1.5 (A:51-90 (gaps) | J:51-90 | - | -)
Exon 1.6 (A:91-157 | J:91-157 | - | -)
Exon 1.9b (A:157-197 (gaps) | J:157-197 (gaps...)
Exon 1.10 (A:197-246 | J:197-246 | - | -)
Exon 1.11 (A:247-279 | J:247-279 | - | -)
Exon 1.12b (A:280-329 | J:280-329 | - | -)
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All Exon Boundaries
01: Boundary -/1.2a
02: Boundary 1.2a/1.3
03: Boundary 1.3/1.4c
04: Boundary 1.4c/1.5
05: Boundary 1.5/1.6
06: Boundary 1.6/1.9b
07: Boundary 1.9b/1.10
08: Boundary 1.10/1.11
09: Boundary 1.11/1.12b
10: Boundary 1.12b/-
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.2a
ENST00000373025
2a
ENSE00001958407
chr6:
41715135-41715014
122
PEPC_HUMAN
1-20
20
2
-
-
P:1-4
Q:1-4
-
-
4
4
1.3
ENST00000373025
3
ENSE00000750752
chr6:
41712546-41712396
151
PEPC_HUMAN
20-70
51
4
A:2-11
J:2-11
P:4-21
Q:4-22
10
10
18
19
1.4c
ENST00000373025
4c
ENSE00002162675
chr6:
41712252-41712135
118
PEPC_HUMAN
71-110
40
2
A:12-51
J:12-51
-
-
40
40
-
-
1.5
ENST00000373025
5
ENSE00002167075
chr6:
41711127-41711009
119
PEPC_HUMAN
110-149
40
2
A:51-90 (gaps)
J:51-90
-
-
40
40
-
-
1.6
ENST00000373025
6
ENSE00002151094
chr6:
41710227-41710028
200
PEPC_HUMAN
150-216
67
2
A:91-157
J:91-157
-
-
67
67
-
-
1.9b
ENST00000373025
9b
ENSE00002190311
chr6:
41708348-41708229
120
PEPC_HUMAN
216-256
41
2
A:157-197 (gaps)
J:157-197 (gaps)
-
-
41
41
-
-
1.10
ENST00000373025
10
ENSE00002152293
chr6:
41707684-41707537
148
PEPC_HUMAN
256-305
50
2
A:197-246
J:197-246
-
-
50
50
-
-
1.11
ENST00000373025
11
ENSE00002188870
chr6:
41705566-41705468
99
PEPC_HUMAN
306-338
33
2
A:247-279
J:247-279
-
-
33
33
-
-
1.12b
ENST00000373025
12b
ENSE00001814259
chr6:
41704742-41704449
294
PEPC_HUMAN
339-388
50
2
A:280-329
J:280-329
-
-
50
50
-
-
[
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SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1avf_1 (P:,A:)
1b: SCOP_d1avf_2 (Q:,J:)
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Classes
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)
(
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)
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(
)
Protein Domains
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)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Acid proteases
(1120)
Superfamily
:
Acid proteases
(1120)
Family
:
Pepsin-like
(505)
Protein domain
:
Pepsin(ogen)
(16)
Human (Homo sapiens), progastricsin (pepsinogen C) [TaxId: 9606]
(2)
1a
d1avf.1
P:,A:
1b
d1avf.2
Q:,J:
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1avfA02 (A:172-327)
1b: CATH_1avfJ02 (J:172-328)
1c: CATH_1avfA01 (A:2-171)
1d: CATH_1avfJ01 (J:2-171)
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)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Cathepsin D, subunit A; domain 1
(745)
Homologous Superfamily
:
Acid Proteases
(745)
Human (Homo sapiens)
(161)
1a
1avfA02
A:172-327
1b
1avfJ02
J:172-328
1c
1avfA01
A:2-171
1d
1avfJ01
J:2-171
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Pfam Domains
(0, 0)
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all PFAM domains
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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 (121 KB)
Header - Asym.Unit
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