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2DJF
Biol. Unit 1
Info
Asym.Unit (69 KB)
Biol.Unit 1 (246 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN DIPEPTIDYL PEPTIDASE I (CATHEPSIN C) IN COMPLEX WITH THE INHIBITOR GLY-PHE-CHN2
Authors
:
A. Molgaard, J. Arnau, C. Lauritzen, S. Larsen, G. Petersen, J. Pederse
Date
:
02 Apr 06 (Deposition) - 14 Nov 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (4x)
Keywords
:
Protein-Inhibitor Complex, Covalently Bound Inhibitor, Dppi-Inhibitor Complex, Cathepsin C Inhibitor Complex, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Molgaard, J. Arnau, C. Lauritzen, S. Larsen, G. Petersen, J. Pedersen
The Crystal Structure Of Human Dipeptidyl Peptidase I (Cathepsin C) In Complex With The Inhibitor Gly-Phe-Chn2
Biochem. J. V. 401 645 2007
[
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Hetero Components
(3, 24)
Info
All Hetero Components
1a: N-[(1S)-1-BENZYL-3-DIAZEN-1-IUMYLI... (1ZBa)
2a: ACETIC ACID (ACYa)
3a: CHLORIDE ION (CLa)
4a: N-ACETYL-D-GLUCOSAMINE (NAGa)
4b: N-ACETYL-D-GLUCOSAMINE (NAGb)
4c: N-ACETYL-D-GLUCOSAMINE (NAGc)
4d: N-ACETYL-D-GLUCOSAMINE (NAGd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1ZB
4
Ligand/Ion
N-[(1S)-1-BENZYL-3-DIAZEN-1-IUMYLIDENE-2-OXOPROPYL]GLYCINAMIDE
2
ACY
4
Ligand/Ion
ACETIC ACID
3
CL
-1
Ligand/Ion
CHLORIDE ION
4
NAG
16
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
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
ASN A:5 , ASN A:65 , HOH A:716 , HOH A:746
BINDING SITE FOR RESIDUE NAG A 601
2
AC2
SOFTWARE
ASN A:95
BINDING SITE FOR RESIDUE NAG A 602
3
AC3
SOFTWARE
ASN A:29 , SER A:31
BINDING SITE FOR RESIDUE NAG A 603
4
AC4
SOFTWARE
LEU B:207 , ASN B:252
BINDING SITE FOR RESIDUE NAG B 604
5
AC5
SOFTWARE
PHE B:278 , PRO B:279 , TYR B:280 , TYR B:323
BINDING SITE FOR RESIDUE CL B 500
6
AC6
SOFTWARE
ASP A:1 , GLN B:228 , GLY B:232 , SER B:233 , CYS B:234 , GLU B:275 , GLY B:276 , GLY B:277 , PHE B:278 , HOH C:112 , ASN C:380 , HIS C:381
BINDING SITE FOR RESIDUE 1ZB B 801
7
AC7
SOFTWARE
SER A:22 , GLY A:23 , LYS A:38 , TYR A:75 , LYS C:438 , LEU C:439
BINDING SITE FOR RESIDUE ACY A 700
[
close Site info
]
SAPs(SNPs)/Variants
(29, 116)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_016933 (W15S, chain A, )
02: VAR_016934 (H103P, chain A, )
03: VAR_019036 (V105E, chain A, )
04: VAR_019037 (G115R, chain A, )
05: VAR_019038 (D212Y, chain B, )
06: VAR_009541 (V225F, chain B, )
07: VAR_009542 (Q228L, chain B, )
08: VAR_019039 (R248H, chain B, )
09: VAR_009543 (R248P, chain B, )
10: VAR_016935 (Q262R, chain B, )
11: VAR_019040 (C267Y, chain B, )
12: VAR_039686 (Y270H, chain B, )
13: VAR_019041 (G276D, chain B, )
14: VAR_019042 (G276S, chain B, )
15: VAR_009544 (G277S, chain B, )
16: VAR_019043 (G277V, chain B, )
17: VAR_019044 (Y280N, chain B, )
18: VAR_019045 (Q288R, chain B, )
19: VAR_019046 (E295G, chain B, )
20: VAR_009545 (R315C, chain B, )
21: VAR_016944 (Y316C, chain B, )
22: VAR_009546 (Y323C, chain B, )
23: VAR_016945 (E377K, chain C, )
24: VAR_027249 (H381N, chain C, )
25: VAR_027250 (H381R, chain C, )
26: VAR_019047 (Y388C, chain C, )
27: VAR_016936 (W405C, chain C, )
28: VAR_019048 (E423G, chain C, )
29: VAR_016946 (I429V, chain C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_016933
W
39
S
CATC_HUMAN
Disease (PLS)
---
A
W
15
S
02
UniProt
VAR_016934
H
127
P
CATC_HUMAN
Disease (PLS)
---
A
H
103
P
03
UniProt
VAR_019036
V
129
E
CATC_HUMAN
Disease (PLS)
---
A
V
105
E
04
UniProt
VAR_019037
G
139
R
CATC_HUMAN
Disease (PLS)
---
A
G
115
R
05
UniProt
VAR_019038
D
236
Y
CATC_HUMAN
Disease (PLS)
---
B
D
212
Y
06
UniProt
VAR_009541
V
249
F
CATC_HUMAN
Disease (PLS)
---
B
V
225
F
07
UniProt
VAR_009542
Q
252
L
CATC_HUMAN
Disease (PLS)
---
B
Q
228
L
08
UniProt
VAR_019039
R
272
H
CATC_HUMAN
Disease (PLS)
---
B
R
248
H
09
UniProt
VAR_009543
R
272
P
CATC_HUMAN
Disease (PLS)
---
B
R
248
P
10
UniProt
VAR_016935
Q
286
R
CATC_HUMAN
Disease (PLS)
---
B
Q
262
R
11
UniProt
VAR_019040
C
291
Y
CATC_HUMAN
Disease (PLS)
---
B
C
267
Y
12
UniProt
VAR_039686
Y
294
H
CATC_HUMAN
Disease (PLS)
---
B
Y
270
H
13
UniProt
VAR_019041
G
300
D
CATC_HUMAN
Disease (PLS)
---
B
G
276
D
14
UniProt
VAR_019042
G
300
S
CATC_HUMAN
Disease (PLS)
---
B
G
276
S
15
UniProt
VAR_009544
G
301
S
CATC_HUMAN
Disease (PLS)
---
B
G
277
S
16
UniProt
VAR_019043
G
301
V
CATC_HUMAN
Disease (PLS)
---
B
G
277
V
17
UniProt
VAR_019044
Y
304
N
CATC_HUMAN
Disease (PLS)
---
B
Y
280
N
18
UniProt
VAR_019045
Q
312
R
CATC_HUMAN
Disease (PLS)
---
B
Q
288
R
19
UniProt
VAR_019046
E
319
G
CATC_HUMAN
Disease (PLS)
---
B
E
295
G
20
UniProt
VAR_009545
R
339
C
CATC_HUMAN
Disease (PLS)
---
B
R
315
C
21
UniProt
VAR_016944
Y
340
C
CATC_HUMAN
Disease (PLS)
---
B
Y
316
C
22
UniProt
VAR_009546
Y
347
C
CATC_HUMAN
Disease (AP1)
---
B
Y
323
C
23
UniProt
VAR_016945
E
401
K
CATC_HUMAN
Polymorphism
---
C
E
377
K
24
UniProt
VAR_027249
H
405
N
CATC_HUMAN
Disease (PLS)
---
C
H
381
N
25
UniProt
VAR_027250
H
405
R
CATC_HUMAN
Disease (PLS)
151269219
C
H
381
R
26
UniProt
VAR_019047
Y
412
C
CATC_HUMAN
Disease (AP1)
28937571
C
Y
388
C
27
UniProt
VAR_016936
W
429
C
CATC_HUMAN
Disease (PLS)
---
C
W
405
C
28
UniProt
VAR_019048
E
447
G
CATC_HUMAN
Disease (PLS)
---
C
E
423
G
29
UniProt
VAR_016946
I
453
V
CATC_HUMAN
Polymorphism
3888798
C
I
429
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 12)
Info
All PROSITE Patterns/Profiles
1: THIOL_PROTEASE_CYS (B:228-239)
2: THIOL_PROTEASE_HIS (C:379-389)
3: THIOL_PROTEASE_ASN (C:398-417)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
THIOL_PROTEASE_CYS
PS00139
Eukaryotic thiol (cysteine) proteases cysteine active site.
CATC_HUMAN
252-263
4
B:228-239
2
THIOL_PROTEASE_HIS
PS00639
Eukaryotic thiol (cysteine) proteases histidine active site.
CATC_HUMAN
403-413
4
C:379-389
3
THIOL_PROTEASE_ASN
PS00640
Eukaryotic thiol (cysteine) proteases asparagine active site.
CATC_HUMAN
422-441
4
C:398-417
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
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
(1, 1)
Info
All SCOP Domains
1a: SCOP_d2djfa_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Streptavidin-like
(225)
Superfamily
:
Dipeptidyl peptidase I (cathepsin C), exclusion domain
(9)
Family
:
Dipeptidyl peptidase I (cathepsin C), exclusion domain
(8)
Protein domain
:
Dipeptidyl peptidase I (cathepsin C), exclusion domain
(8)
Human (Homo sapiens) [TaxId: 9606]
(7)
1a
d2djfa_
A:
[
close SCOP info
]
CATH Domains
(3, 3)
Info
all CATH domains
1a: CATH_2djfB01 (B:215-358)
2a: CATH_2djfA00 (A:1-118)
3a: CATH_2djfC00 (C:372-439)
View:
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Classes
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(
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(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Cathepsin B; Chain A
(207)
Homologous Superfamily
:
Cysteine proteinases
(207)
Human (Homo sapiens)
(92)
1a
2djfB01
B:215-358
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Lipocalin
(526)
Homologous Superfamily
:
[code=2.40.128.80, no name defined]
(4)
Human (Homo sapiens)
(3)
2a
2djfA00
A:1-118
Topology
:
OB fold (Dihydrolipoamide Acetyltransferase, E2P)
(1040)
Homologous Superfamily
:
Cysteine proteinases. Chain C
(5)
Human (Homo sapiens)
(5)
3a
2djfC00
C:372-439
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
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Atom Selection
(currently selected atoms:
all
)
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Sidechain
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Solvent
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Protein & NOT Site
Protein & NOT PROSITE
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Chain C
Asymmetric Unit 1
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