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Getting 'Exon' information from database.
4CDC
Asym. Unit
Info
Asym.Unit (470 KB)
Biol.Unit 1 (120 KB)
Biol.Unit 2 (119 KB)
Biol.Unit 3 (119 KB)
Biol.Unit 4 (120 KB)
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(1)
Title
:
HUMAN DPP1 IN COMPLEX WITH (2S)-2-AMINO-N-((1S)-1-CYANO-2-( 4-PHENYLPHENYL)ETHYL)BUTANAMIDE
Authors
:
J. Debreczeni, K. Edman, M. Furber, A. Tiden, P. Gardiner, T. Mete, R. Fo I. Millichip, L. Stein, A. Mather, E. Kinchin, C. Luckhurst, P. Cage, H. Sanghanee, J. Breed, L. Wissler
Date
:
31 Oct 13 (Deposition) - 19 Mar 14 (Release) - 09 Apr 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: G,H,I (1x)
Biol. Unit 2: D,E,F (1x)
Biol. Unit 3: A,B,C (1x)
Biol. Unit 4: J,K,L (1x)
Keywords
:
Hydrolase, Inhibitor
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Furber, P. Gardiner, A. K. Tiden, A. Mete, R. Ford, I. Millichip, L. Stein, A. Mather, E. Kinchin, C. Luckhurst, S. Barber, P. Cage, H. Sanganee, R. Austin, K. Chohan, R. Beri, B. Thong, A. Wallace, V. Oreffo, R. Hutchinson, S. Harper, J. Debreczeni, J. Breed, L. Wissler, K. Edman
Cathepsin C Inhibitors: Property Optimization And Identification Of A Clinical Candidate.
J. Med. Chem. V. 57 2357 2014
[
close entry info
]
Hetero Components
(4, 19)
Info
All Hetero Components
1a: (2S)-2-AZANYL-N-[(2S)-1-AZANYLIDEN... (6AOa)
1b: (2S)-2-AZANYL-N-[(2S)-1-AZANYLIDEN... (6AOb)
1c: (2S)-2-AZANYL-N-[(2S)-1-AZANYLIDEN... (6AOc)
1d: (2S)-2-AZANYL-N-[(2S)-1-AZANYLIDEN... (6AOd)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
6AO
4
Ligand/Ion
(2S)-2-AZANYL-N-[(2S)-1-AZANYLIDENE-3-(4-PHENYLPHENYL)PROPAN-2-YL]BUTANAMIDE
2
CL
4
Ligand/Ion
CHLORIDE ION
3
GOL
4
Ligand/Ion
GLYCEROL
4
NAG
7
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(19, 19)
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)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:1 , GLN B:228 , CYS B:234 , GLU B:275 , GLY B:276 , GLY B:277 , PHE B:278 , ASN C:380
BINDING SITE FOR RESIDUE 6AO B1368
02
AC2
SOFTWARE
PHE B:314 , LYS C:438 , LEU C:439 , SER D:22 , GLY D:23 , TYR D:75 , ASN D:109 , TRP D:110 , ALA D:111
BINDING SITE FOR RESIDUE GOL D1120
03
AC3
SOFTWARE
ASP D:1 , HOH D:2001 , GLN E:228 , GLY E:232 , CYS E:234 , GLY E:276 , GLY E:277 , PHE E:278 , ALA E:349 , ASN F:380 , HIS F:381 , ASP K:354 , LEU K:357 , HIS K:358
BINDING SITE FOR RESIDUE 6AO E1368
04
AC4
SOFTWARE
SER G:57 , GLY G:58 , HIS G:59 , VAL G:71 , ASN G:73 , ASP G:74
BINDING SITE FOR RESIDUE GOL G1121
05
AC5
SOFTWARE
LYS G:76 , VAL G:105 , HOH G:2029 , GLN H:288 , SER H:319 , LEU J:106
BINDING SITE FOR RESIDUE GOL G1122
06
AC6
SOFTWARE
ASP G:1 , HOH G:2001 , GLN H:228 , CYS H:234 , GLU H:275 , GLY H:276 , GLY H:277 , PHE H:278 , ASN I:380
BINDING SITE FOR RESIDUE 6AO H1368
07
AC7
SOFTWARE
ASP E:354 , LEU E:357 , HIS E:358 , ASP J:1 , GLN K:228 , CYS K:234 , GLU K:275 , GLY K:276 , GLY K:277 , PHE K:278 , ALA K:349 , ASN L:380
BINDING SITE FOR RESIDUE 6AO K1368
08
AC8
SOFTWARE
HIS K:322 , VAL K:324 , GLY K:325 , GLY K:326 , LEU K:335 , GLU K:339
BINDING SITE FOR RESIDUE GOL K1370
09
AC9
SOFTWARE
PHE B:278 , TYR B:280 , TYR B:323
BINDING SITE FOR RESIDUE CL B1370
10
BC1
SOFTWARE
PHE E:278 , PRO E:279 , TYR E:280 , TYR E:323 , VAL F:431
BINDING SITE FOR RESIDUE CL E1369
11
BC2
SOFTWARE
PHE H:278 , PRO H:279 , TYR H:280 , TYR H:323 , VAL I:431
BINDING SITE FOR RESIDUE CL H1370
12
BC3
SOFTWARE
PHE K:278 , PRO K:279 , TYR K:280 , TYR K:323
BINDING SITE FOR RESIDUE CL K1371
13
BC4
SOFTWARE
ASN A:5 , ASN A:65 , PHE C:376 , LEU C:378
BINDING SITE FOR MONO-SACCHARIDE NAG A1120 BOUND TO ASN A 5
14
BC5
SOFTWARE
ASN B:252 , LEU H:207 , THR H:209
BINDING SITE FOR MONO-SACCHARIDE NAG B1369 BOUND TO ASN B 252
15
BC6
SOFTWARE
ASN D:5 , HOH D:2003
BINDING SITE FOR MONO-SACCHARIDE NAG D1119 BOUND TO ASN D 5
16
BC7
SOFTWARE
ASN G:5 , ASN G:65 , PHE I:376
BINDING SITE FOR MONO-SACCHARIDE NAG G1120 BOUND TO ASN G 5
17
BC8
SOFTWARE
LEU B:207 , THR B:209 , ASN H:252
BINDING SITE FOR MONO-SACCHARIDE NAG H1369 BOUND TO ASN H 252
18
BC9
SOFTWARE
ASN J:5 , LEU L:378
BINDING SITE FOR MONO-SACCHARIDE NAG J1120 BOUND TO ASN J 5
19
CC1
SOFTWARE
THR E:209 , LEU G:54 , ASN K:252
BINDING SITE FOR MONO-SACCHARIDE NAG K1369 BOUND TO ASN K 252
[
close Site info
]
SAPs(SNPs)/Variants
(29, 116)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_016933 (W15S, chain A/D/G/J, )
02: VAR_016934 (H103P, chain A/D/G/J, )
03: VAR_019036 (V105E, chain A/D/G/J, )
04: VAR_019037 (G115R, chain A/D/G/J, )
05: VAR_019038 (D212Y, chain B/E/H/K, )
06: VAR_009541 (V225F, chain B/E/H/K, )
07: VAR_009542 (Q228L, chain B/E/H/K, )
08: VAR_019039 (R248H, chain B/E/H/K, )
09: VAR_009543 (R248P, chain B/E/H/K, )
10: VAR_016935 (Q262R, chain B/E/H/K, )
11: VAR_019040 (C267Y, chain B/E/H/K, )
12: VAR_039686 (Y270H, chain B/E/H/K, )
13: VAR_019041 (G276D, chain B/E/H/K, )
14: VAR_019042 (G276S, chain B/E/H/K, )
15: VAR_009544 (G277S, chain B/E/H/K, )
16: VAR_019043 (G277V, chain B/E/H/K, )
17: VAR_019044 (Y280N, chain B/E/H/K, )
18: VAR_019045 (Q288R, chain B/E/H/K, )
19: VAR_019046 (E295G, chain B/E/H/K, )
20: VAR_009545 (R315C, chain B/E/H/K, )
21: VAR_016944 (Y316C, chain B/E/H/K, )
22: VAR_009546 (Y323C, chain B/E/H/K, )
23: VAR_016945 (E377K, chain C/F/I/L, )
24: VAR_027249 (H381N, chain C/F/I/L, )
25: VAR_027250 (H381R, chain C/F/I/L, )
26: VAR_019047 (Y388C, chain C/F/I/L, )
27: VAR_016936 (W405C, chain C/F/I/L, )
28: VAR_019048 (E423G, chain C/F/I/L, )
29: VAR_016946 (I429V, chain C/F/I/L, )
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/D/G/J
W
15
S
02
UniProt
VAR_016934
H
127
P
CATC_HUMAN
Disease (PLS)
---
A/D/G/J
H
103
P
03
UniProt
VAR_019036
V
129
E
CATC_HUMAN
Disease (PLS)
---
A/D/G/J
V
105
E
04
UniProt
VAR_019037
G
139
R
CATC_HUMAN
Disease (PLS)
---
A/D/G/J
G
115
R
05
UniProt
VAR_019038
D
236
Y
CATC_HUMAN
Disease (PLS)
---
B/E/H/K
D
212
Y
06
UniProt
VAR_009541
V
249
F
CATC_HUMAN
Disease (PLS)
---
B/E/H/K
V
225
F
07
UniProt
VAR_009542
Q
252
L
CATC_HUMAN
Disease (PLS)
---
B/E/H/K
Q
228
L
08
UniProt
VAR_019039
R
272
H
CATC_HUMAN
Disease (PLS)
---
B/E/H/K
R
248
H
09
UniProt
VAR_009543
R
272
P
CATC_HUMAN
Disease (PLS)
---
B/E/H/K
R
248
P
10
UniProt
VAR_016935
Q
286
R
CATC_HUMAN
Disease (PLS)
---
B/E/H/K
Q
262
R
11
UniProt
VAR_019040
C
291
Y
CATC_HUMAN
Disease (PLS)
---
B/E/H/K
C
267
Y
12
UniProt
VAR_039686
Y
294
H
CATC_HUMAN
Disease (PLS)
---
B/E/H/K
Y
270
H
13
UniProt
VAR_019041
G
300
D
CATC_HUMAN
Disease (PLS)
---
B/E/H/K
G
276
D
14
UniProt
VAR_019042
G
300
S
CATC_HUMAN
Disease (PLS)
---
B/E/H/K
G
276
S
15
UniProt
VAR_009544
G
301
S
CATC_HUMAN
Disease (PLS)
---
B/E/H/K
G
277
S
16
UniProt
VAR_019043
G
301
V
CATC_HUMAN
Disease (PLS)
---
B/E/H/K
G
277
V
17
UniProt
VAR_019044
Y
304
N
CATC_HUMAN
Disease (PLS)
---
B/E/H/K
Y
280
N
18
UniProt
VAR_019045
Q
312
R
CATC_HUMAN
Disease (PLS)
---
B/E/H/K
Q
288
R
19
UniProt
VAR_019046
E
319
G
CATC_HUMAN
Disease (PLS)
---
B/E/H/K
E
295
G
20
UniProt
VAR_009545
R
339
C
CATC_HUMAN
Disease (PLS)
---
B/E/H/K
R
315
C
21
UniProt
VAR_016944
Y
340
C
CATC_HUMAN
Disease (PLS)
---
B/E/H/K
Y
316
C
22
UniProt
VAR_009546
Y
347
C
CATC_HUMAN
Disease (AP1)
---
B/E/H/K
Y
323
C
23
UniProt
VAR_016945
E
401
K
CATC_HUMAN
Polymorphism
---
C/F/I/L
E
377
K
24
UniProt
VAR_027249
H
405
N
CATC_HUMAN
Disease (PLS)
---
C/F/I/L
H
381
N
25
UniProt
VAR_027250
H
405
R
CATC_HUMAN
Disease (PLS)
151269219
C/F/I/L
H
381
R
26
UniProt
VAR_019047
Y
412
C
CATC_HUMAN
Disease (AP1)
28937571
C/F/I/L
Y
388
C
27
UniProt
VAR_016936
W
429
C
CATC_HUMAN
Disease (PLS)
---
C/F/I/L
W
405
C
28
UniProt
VAR_019048
E
447
G
CATC_HUMAN
Disease (PLS)
---
C/F/I/L
E
423
G
29
UniProt
VAR_016946
I
453
V
CATC_HUMAN
Polymorphism
3888798
C/F/I/L
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,E:228-239,H:228-239,K:22...)
2: THIOL_PROTEASE_HIS (C:379-389,F:379-389,I:379-389,L:37...)
3: THIOL_PROTEASE_ASN (C:398-417,F:398-417,I:398-417,L:39...)
;
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
E:228-239
H:228-239
K:228-239
2
THIOL_PROTEASE_HIS
PS00639
Eukaryotic thiol (cysteine) proteases histidine active site.
CATC_HUMAN
403-413
4
C:379-389
F:379-389
I:379-389
L:379-389
3
THIOL_PROTEASE_ASN
PS00640
Eukaryotic thiol (cysteine) proteases asparagine active site.
CATC_HUMAN
422-441
4
C:398-417
F:398-417
I:398-417
L:398-417
[
close PROSITE info
]
Exons
(6, 28)
Info
All Exons
Exon 1.1a (A:1-34 | - | - | D:1-34 | - | - | ...)
Exon 1.2a (A:34-82 | - | - | D:34-82 | - | - ...)
Exon 1.6 (A:83-119 (gaps) | - | - | D:83-118...)
Exon 1.8 (- | B:206-229 | - | - | E:206-229 ...)
Exon 1.9c (- | B:229-273 | - | - | E:229-273 ...)
Exon 1.10b (- | B:273-367 | C:372-439 | - | E:...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1a
2: Boundary 1.1a/1.2a
3: Boundary 1.2a/1.6
4: Boundary 1.6/1.7b
5: Boundary 1.7b/1.8
6: Boundary 1.8/1.9c
7: Boundary 1.9c/1.10b
8: Boundary 1.10b/-
View:
Label:
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
1.1a
ENST00000227266
1a
ENSE00002140483
chr11:
88070955-88070669
287
CATC_HUMAN
1-58
58
4
A:1-34
-
-
D:1-34
-
-
G:1-34
-
-
J:1-34
-
-
34
-
-
34
-
-
34
-
-
34
-
-
1.2a
ENST00000227266
2a
ENSE00000743353
chr11:
88068250-88068105
146
CATC_HUMAN
58-106
49
4
A:34-82
-
-
D:34-82
-
-
G:34-82
-
-
J:34-82
-
-
49
-
-
49
-
-
49
-
-
49
-
-
1.6
ENST00000227266
6
ENSE00000743352
chr11:
88045722-88045556
167
CATC_HUMAN
107-162
56
4
A:83-119 (gaps)
-
-
D:83-118 (gaps)
-
-
G:83-119 (gaps)
-
-
J:83-119 (gaps)
-
-
37
-
-
36
-
-
37
-
-
37
-
-
1.7b
ENST00000227266
7b
ENSE00000743351
chr11:
88042486-88042331
156
CATC_HUMAN
162-214
53
0
-
-
1.8
ENST00000227266
8
ENSE00000743350
chr11:
88033813-88033698
116
CATC_HUMAN
214-253
40
4
-
B:206-229
-
-
E:206-229
-
-
H:206-229
-
-
K:206-229
-
-
24
-
-
24
-
-
24
-
-
24
-
1.9c
ENST00000227266
9c
ENSE00000743349
chr11:
88029432-88029301
132
CATC_HUMAN
253-297
45
4
-
B:229-273
-
-
E:229-273
-
-
H:229-273
-
-
K:229-273
-
-
45
-
-
45
-
-
45
-
-
45
-
1.10b
ENST00000227266
10b
ENSE00000842724
chr11:
88027676-88026778
899
CATC_HUMAN
297-463
167
8
-
B:273-367
C:372-439
-
E:273-367 (gaps)
F:372-439
-
H:273-367
I:372-439
-
K:273-367
L:372-439
-
95
68
-
95
68
-
95
68
-
95
68
[
close EXON info
]
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d4cdca_ (A:)
1b: SCOP_d4cdcj_ (J:)
1c: SCOP_d4cdcd_ (D:)
1d: SCOP_d4cdcg_ (G:)
View:
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)
(
)
Folds
(
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(
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(
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(
)
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(
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(
)
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
d4cdca_
A:
1b
d4cdcj_
J:
1c
d4cdcd_
D:
1d
d4cdcg_
G:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
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Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
Chain I
Chain J
Chain K
Chain L
Asymmetric Unit 1
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Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
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