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3BN9
Asym. Unit
Info
Asym.Unit (451 KB)
Biol.Unit 1 (223 KB)
Biol.Unit 2 (226 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF MT-SP1 IN COMPLEX WITH FAB INHIBITOR E2
Authors
:
C. J. Farady, E. L. Schneider, P. F. Egea, D. H. Goetz, C. S. Craik
Date
:
13 Dec 07 (Deposition) - 09 Sep 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.17
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: B,C,D (1x)
Biol. Unit 2: A,E,F (1x)
Keywords
:
Antibody-Protease Complex, Protein-Protein Complex, Enzyme- Inhibitor Complex, Disease Mutation, Glycoprotein, Hydrolase, Membrane, Polymorphism, Serine Protease, Signal- Anchor, Transmembrane
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. J. Farady, P. F. Egea, E. L. Schneider, M. R. Darragh, C. S. Craik
Structure Of An Fab-Protease Complex Reveals A Highly Specific Non-Canonical Mechanism Of Inhibition
J. Mol. Biol. V. 380 351 2008
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 15)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
1f: 1,2-ETHANEDIOL (EDOf)
1g: 1,2-ETHANEDIOL (EDOg)
1h: 1,2-ETHANEDIOL (EDOh)
1i: 1,2-ETHANEDIOL (EDOi)
1j: 1,2-ETHANEDIOL (EDOj)
1k: 1,2-ETHANEDIOL (EDOk)
1l: 1,2-ETHANEDIOL (EDOl)
1m: 1,2-ETHANEDIOL (EDOm)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
13
Ligand/Ion
1,2-ETHANEDIOL
2
SO4
2
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(15, 15)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS B:91 , LEU B:233 , PHE B:234 , TRP B:237 , HOH B:381 , HOH B:420
BINDING SITE FOR RESIDUE EDO B 1
02
AC2
SOFTWARE
GLY B:25 , GLU B:26 , TRP B:27 , PRO B:28 , HIS B:71 , MET B:117 , HOH B:448
BINDING SITE FOR RESIDUE EDO B 3
03
AC3
SOFTWARE
PHE B:184A , LEU B:185 , SER B:186 , HOH B:384 , HOH B:508
BINDING SITE FOR RESIDUE EDO B 4
04
AC4
SOFTWARE
ARG B:230 , PRO B:232 , LEU B:233 , HOH B:367
BINDING SITE FOR RESIDUE EDO B 6
05
AC5
SOFTWARE
GLU B:26 , TRP B:29 , ILE B:207
BINDING SITE FOR RESIDUE EDO B 7
06
AC6
SOFTWARE
ALA B:135 , ARG B:161 , HOH B:496 , HOH B:516
BINDING SITE FOR RESIDUE EDO B 8
07
AC7
SOFTWARE
GLN C:37 , LYS C:39 , LYS C:42 , LYS C:45 , HOH C:337
BINDING SITE FOR RESIDUE SO4 C 215
08
AC8
SOFTWARE
SER C:65 , GLY C:66 , ASP C:70 , PHE C:71 , THR C:72
BINDING SITE FOR RESIDUE EDO C 216
09
AC9
SOFTWARE
GLY B:18 , VAL C:110 , ALA C:111 , ALA C:112
BINDING SITE FOR RESIDUE EDO C 217
10
BC1
SOFTWARE
TYR C:96 , GLN D:100F , ASN D:100G , VAL D:100H , SER D:100I , PHE D:100K , HOH D:287
BINDING SITE FOR RESIDUE EDO D 243
11
BC2
SOFTWARE
PHE A:184A , LEU A:185 , SER A:186
BINDING SITE FOR RESIDUE EDO A 2
12
BC3
SOFTWARE
PRO A:178 , ARG A:179
BINDING SITE FOR RESIDUE EDO A 12
13
BC4
SOFTWARE
HIS A:91 , TYR A:101 , PHE A:234 , TRP A:237
BINDING SITE FOR RESIDUE EDO A 13
14
BC5
SOFTWARE
GLN E:37 , LYS E:39 , LYS E:42 , LYS E:45
BINDING SITE FOR RESIDUE SO4 E 215
15
BC6
SOFTWARE
GLN E:38 , GLY E:41 , LYS E:42 , TYR F:91
BINDING SITE FOR RESIDUE EDO E 216
[
close Site info
]
SAPs(SNPs)/Variants
(5, 10)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_073326 (V5L, chain D/F, )
2: VAR_073327 (A60G, chain D/F, )
3: VAR_066403 (W148R, chain C/E, )
4: VAR_003897 (V191L, chain C/E, )
5: VAR_032849 (G216R, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_073326
V
24
L
HV303_HUMAN
Polymorphism
---
D/F
V
5
L
2
UniProt
VAR_073327
A
80
G
HV303_HUMAN
Polymorphism
---
D/F
A
60
G
3
UniProt
VAR_066403
W
40
R
IGKC_HUMAN
Disease (IGKCD)
---
C/E
W
148
R
4
UniProt
VAR_003897
V
83
L
IGKC_HUMAN
Unclassified
---
C/E
V
191
L
5
UniProt
VAR_032849
G
827
R
ST14_HUMAN
Disease (ARCI11)
---
A/B
G
216
R
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(4, 8)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (C:192-198,E:192-198)
2: TRYPSIN_DOM (A:16-243,B:16-243)
3: TRYPSIN_HIS (A:53-58,B:53-58)
4: TRYPSIN_SER (A:189-200,B:189-200)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
IG_MHC
PS00290
Immunoglobulins and major histocompatibility complex proteins signature.
IGKC_HUMAN
85-91
2
C:192-198
E:192-198
2
TRYPSIN_DOM
PS50240
Serine proteases, trypsin domain profile.
ST14_HUMAN
615-854
2
A:16-243
B:16-243
3
TRYPSIN_HIS
PS00134
Serine proteases, trypsin family, histidine active site.
ST14_HUMAN
652-657
2
A:53-58
B:53-58
4
TRYPSIN_SER
PS00135
Serine proteases, trypsin family, serine active site.
ST14_HUMAN
799-810
2
A:189-200
B:189-200
[
close PROSITE info
]
Exons
(5, 10)
Info
All Exons
Exon 1.16 (A:16-60F | B:16-60F)
Exon 1.17 (A:60F-148 | B:60F-148)
Exon 1.18 (A:148-192 (gaps) | B:148-192 (gaps...)
Exon 1.19b (A:193-244 (gaps) | B:193-244 (gaps...)
Exon 2.2 (D:1-93 | F:1-93)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.15/1.16
2: Boundary 1.16/1.17
3: Boundary 1.17/1.18
4: Boundary 1.18/1.19b
5: Boundary 1.19b/-
6: Boundary 2.1/2.2
7: Boundary 2.2/-
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
ENST00000278742
1a
ENSE00001334626
chr11:
130029457-130029955
499
ST14_HUMAN
1-27
27
0
-
-
1.2
ENST00000278742
2
ENSE00000990418
chr11:
130058009-130058168
160
ST14_HUMAN
28-81
54
0
-
-
1.3
ENST00000278742
3
ENSE00000990419
chr11:
130058425-130058552
128
ST14_HUMAN
81-123
43
0
-
-
1.4
ENST00000278742
4
ENSE00000990421
chr11:
130058764-130058834
71
ST14_HUMAN
124-147
24
0
-
-
1.5c
ENST00000278742
5c
ENSE00000990422
chr11:
130059634-130059791
158
ST14_HUMAN
147-200
54
0
-
-
1.6b
ENST00000278742
6b
ENSE00000990423
chr11:
130060008-130060043
36
ST14_HUMAN
200-212
13
0
-
-
1.7b
ENST00000278742
7b
ENSE00001278516
chr11:
130060349-130060589
241
ST14_HUMAN
212-292
81
0
-
-
1.8
ENST00000278742
8
ENSE00000990429
chr11:
130064044-130064183
140
ST14_HUMAN
292-339
48
0
-
-
1.9
ENST00000278742
9
ENSE00000990430
chr11:
130064535-130064632
98
ST14_HUMAN
339-371
33
0
-
-
1.10b
ENST00000278742
10b
ENSE00000990431
chr11:
130066234-130066343
110
ST14_HUMAN
372-408
37
0
-
-
1.11b
ENST00000278742
11b
ENSE00000990432
chr11:
130066465-130066595
131
ST14_HUMAN
408-452
45
0
-
-
1.12
ENST00000278742
12
ENSE00000990433
chr11:
130067736-130067840
105
ST14_HUMAN
452-487
36
0
-
-
1.13
ENST00000278742
13
ENSE00000990434
chr11:
130068203-130068313
111
ST14_HUMAN
487-524
38
0
-
-
1.14
ENST00000278742
14
ENSE00000990435
chr11:
130068403-130068516
114
ST14_HUMAN
524-562
39
0
-
-
1.15
ENST00000278742
15
ENSE00000990436
chr11:
130068842-130068964
123
ST14_HUMAN
562-603
42
0
-
-
1.16
ENST00000278742
16
ENSE00000990437
chr11:
130069846-130070032
187
ST14_HUMAN
603-665
63
2
A:16-60F
B:16-60F
51
51
1.17
ENST00000278742
17
ENSE00000990438
chr11:
130078305-130078579
275
ST14_HUMAN
665-757
93
2
A:60F-148
B:60F-148
93
93
1.18
ENST00000278742
18
ENSE00000990439
chr11:
130079337-130079473
137
ST14_HUMAN
757-802
46
2
A:148-192 (gaps)
B:148-192 (gaps)
47
47
1.19b
ENST00000278742
19b
ENSE00000990440
chr11:
130079557-130080271
715
ST14_HUMAN
803-855
53
2
A:193-244 (gaps)
B:193-244 (gaps)
54
54
2.1
ENST00000390609
1
ENSE00002048341
chr14:
106725733-106725609
125
HV323_HUMAN
1-16
16
0
-
-
2.2
ENST00000390609
2
ENSE00001851371
chr14:
106725505-106725201
305
HV323_HUMAN
16-116
101
2
D:1-93
F:1-93
97
97
[
close EXON info
]
SCOP Domains
(5, 10)
Info
All SCOP Domains
1a: SCOP_d3bn9c1 (C:1-107)
1b: SCOP_d3bn9e1 (E:1-107)
2a: SCOP_d3bn9c2 (C:108-210)
2b: SCOP_d3bn9e2 (E:108-211)
3a: SCOP_d3bn9d2 (D:114-214)
3b: SCOP_d3bn9f2 (F:114-214)
4a: SCOP_d3bn9d1 (D:1-113)
4b: SCOP_d3bn9f1 (F:1-113)
5a: SCOP_d3bn9a_ (A:)
5b: SCOP_d3bn9b_ (B:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
automated matches
(864)
Protein domain
:
automated matches
(864)
Human (Homo sapiens) [TaxId: 9606]
(448)
1a
d3bn9c1
C:1-107
1b
d3bn9e1
E:1-107
Family
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
automated matches
(652)
Human (Homo sapiens) [TaxId: 9606]
(334)
2a
d3bn9c2
C:108-210
2b
d3bn9e2
E:108-211
Protein domain
:
Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma
(608)
Human (Homo sapiens) [TaxId: 9606]
(179)
3a
d3bn9d2
D:114-214
3b
d3bn9f2
F:114-214
Family
:
V set domains (antibody variable domain-like)
(1919)
Protein domain
:
Camelid IG heavy chain variable domain, VHh
(28)
Human (Homo sapiens) [TaxId: 9606]
(2)
4a
d3bn9d1
D:1-113
4b
d3bn9f1
F:1-113
Fold
:
Trypsin-like serine proteases
(1752)
Superfamily
:
Trypsin-like serine proteases
(1752)
Family
:
Eukaryotic proteases
(1343)
Protein domain
:
Matriptase MTSP1
(16)
Human (Homo sapiens) [TaxId: 9606]
(16)
5a
d3bn9a_
A:
5b
d3bn9b_
B:
[
close SCOP info
]
CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_3bn9A02 (A:28-120,A:233-244)
1b: CATH_3bn9B02 (B:28-120,B:233-244)
1c: CATH_3bn9A01 (A:16-27,A:121-232)
1d: CATH_3bn9B01 (B:16-27,B:121-232)
2a: CATH_3bn9E02 (E:108-211)
2b: CATH_3bn9F02 (F:114-213)
2c: CATH_3bn9D02 (D:114-213)
2d: CATH_3bn9D01 (D:1-113)
2e: CATH_3bn9F01 (F:1-113)
2f: CATH_3bn9C02 (C:108-210)
2g: CATH_3bn9C01 (C:1-107)
2h: CATH_3bn9E01 (E:1-107)
View:
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Topologies
(
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(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Thrombin, subunit H
(1535)
Homologous Superfamily
:
Trypsin-like serine proteases
(1488)
Human (Homo sapiens)
(615)
1a
3bn9A02
A:28-120,A:233-244
1b
3bn9B02
B:28-120,B:233-244
1c
3bn9A01
A:16-27,A:121-232
1d
3bn9B01
B:16-27,B:121-232
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
2a
3bn9E02
E:108-211
2b
3bn9F02
F:114-213
2c
3bn9D02
D:114-213
2d
3bn9D01
D:1-113
2e
3bn9F01
F:1-113
2f
3bn9C02
C:108-210
2g
3bn9C01
C:1-107
2h
3bn9E01
E:1-107
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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