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3S9C
Asym. Unit
Info
Asym.Unit (51 KB)
Biol.Unit 1 (46 KB)
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(1)
Title
:
RUSSELL'S VIPER VENOM SERINE PROTEINASE, RVV-V IN COMPLEX WITH THE FRAGMENT (RESIDUES 1533-1546) OF HUMAN FACTOR V
Authors
:
D. Nakayama, Y. Ben Ammar, S. Takeda
Date
:
01 Jun 11 (Deposition) - 07 Sep 11 (Release) - 03 Jul 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Serine Proteinase, Double Six-Stranded Beta-Barrels, Hydrolase, Glycosylation
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Nakayama, Y. Ben Ammar, T. Miyata, S. Takeda
Structural Basis Of Coagulation Factor V Recognition For Cleavage By Rvv-V
Febs Lett. V. 585 3020 2011
(for further references see the
PDB file header
)
[
close entry info
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Hetero Components
(6, 12)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
2a: BETA-D-GLUCOSE (BGCa)
3a: BETA-D-MANNOSE (BMAa)
4a: ALPHA-D-GLUCOSE (GLCa)
5a: N-ACETYL-D-GLUCOSAMINE (NAGa)
5b: N-ACETYL-D-GLUCOSAMINE (NAGb)
6a: ZINC ION (ZNa)
6b: ZINC ION (ZNb)
6c: ZINC ION (ZNc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
4
Ligand/Ion
ACETATE ION
2
BGC
1
Ligand/Ion
BETA-D-GLUCOSE
3
BMA
1
Ligand/Ion
BETA-D-MANNOSE
4
GLC
1
Ligand/Ion
ALPHA-D-GLUCOSE
5
NAG
2
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
6
ZN
3
Ligand/Ion
ZINC ION
[
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]
Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:245 , NAG A:802
BINDING SITE FOR RESIDUE NAG A 801
02
AC2
SOFTWARE
NAG A:801 , BMA A:803
BINDING SITE FOR RESIDUE NAG A 802
03
AC3
SOFTWARE
HOH A:405 , HOH A:411 , NAG A:802
BINDING SITE FOR RESIDUE BMA A 803
04
AC4
SOFTWARE
TYR A:34 , SER A:38 , ILE A:40 , LYS A:67 , MET A:70 , LYS A:73 , HOH A:251 , HOH A:342
BINDING SITE FOR RESIDUE BGC A 701
05
AC5
SOFTWARE
ARG A:135 , ARG A:137 , ASN A:159 , CYS A:201 , ASN A:202 , GLY A:207
BINDING SITE FOR RESIDUE GLC A 702
06
AC6
SOFTWARE
LYS A:143 , THR A:146 , CYS A:191 , HIS A:192 , GLU A:218 , PRO A:219 , CYS A:220 , HIS A:222 , ZN A:501
BINDING SITE FOR RESIDUE ACT A 901
07
AC7
SOFTWARE
ILE A:144 , HIS A:156 , HOH A:326 , HOH A:367 , ZN A:502
BINDING SITE FOR RESIDUE ACT A 902
08
AC8
SOFTWARE
ASN A:25 , THR A:116 , HIS A:117 , HOH A:388 , ZN A:503 , ACT A:904
BINDING SITE FOR RESIDUE ACT A 903
09
AC9
SOFTWARE
ILE A:24 , ASN A:25 , HIS A:117 , HOH A:283 , ZN A:503 , ACT A:903
BINDING SITE FOR RESIDUE ACT A 904
10
BC1
SOFTWARE
HIS A:192 , GLU A:218 , HIS A:222 , ACT A:901
BINDING SITE FOR RESIDUE ZN A 501
11
BC2
SOFTWARE
HOH A:150 , HIS A:156 , HOH A:367 , HOH A:368 , ACT A:902
BINDING SITE FOR RESIDUE ZN A 502
12
BC3
SOFTWARE
ASN A:25 , HIS A:117 , ACT A:903 , ACT A:904
BINDING SITE FOR RESIDUE ZN A 503
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(3, 3)
Info
All PROSITE Patterns/Profiles
1: TRYPSIN_DOM (A:16-243)
2: TRYPSIN_HIS (A:53-58)
3: TRYPSIN_SER (A:189-200)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TRYPSIN_DOM
PS50240
Serine proteases, trypsin domain profile.
VSPG_DABSI
25-251
1
A:16-243
2
TRYPSIN_HIS
PS00134
Serine proteases, trypsin family, histidine active site.
VSPG_DABSI
63-68
1
A:53-58
3
TRYPSIN_SER
PS00135
Serine proteases, trypsin family, serine active site.
VSPG_DABSI
200-211
1
A:189-200
[
close PROSITE info
]
Exons
(1, 1)
Info
All Exons
Exon 1.13 (B:1539-1545)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.12b/1.13
2: Boundary 1.13/1.14
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
1.1
ENST00000367797
1
ENSE00001673787
chr1:
169555826-169555467
360
FA5_HUMAN
1-53
53
0
-
-
1.2
ENST00000367797
2
ENSE00000789613
chr1:
169551760-169551669
92
FA5_HUMAN
53-84
32
0
-
-
1.3
ENST00000367797
3
ENSE00000789612
chr1:
169541581-169541459
123
FA5_HUMAN
84-125
42
0
-
-
1.4
ENST00000367797
4
ENSE00000789611
chr1:
169530004-169529792
213
FA5_HUMAN
125-196
72
0
-
-
1.5
ENST00000367797
5
ENSE00000789610
chr1:
169528534-169528391
144
FA5_HUMAN
196-244
49
0
-
-
1.6
ENST00000367797
6
ENSE00001435704
chr1:
169526105-169525884
222
FA5_HUMAN
244-318
75
0
-
-
1.7
ENST00000367797
7
ENSE00001435673
chr1:
169524585-169524420
166
FA5_HUMAN
318-373
56
0
-
-
1.8
ENST00000367797
8
ENSE00000789607
chr1:
169521972-169521795
178
FA5_HUMAN
373-432
60
0
-
-
1.9
ENST00000367797
9
ENSE00000789606
chr1:
169519977-169519878
100
FA5_HUMAN
433-466
34
0
-
-
1.10
ENST00000367797
10
ENSE00000789605
chr1:
169519253-169519039
215
FA5_HUMAN
466-537
72
0
-
-
1.11
ENST00000367797
11
ENSE00000789604
chr1:
169515830-169515680
151
FA5_HUMAN
538-588
51
0
-
-
1.12b
ENST00000367797
12b
ENSE00000789603
chr1:
169513746-169513534
213
FA5_HUMAN
588-659
72
0
-
-
1.13
ENST00000367797
13
ENSE00000814494
chr1:
169512352-169509532
2821
FA5_HUMAN
659-1599
941
1
B:1539-1545
7
1.14
ENST00000367797
14
ENSE00000814495
chr1:
169505918-169505744
175
FA5_HUMAN
1599-1657
59
0
-
-
1.15
ENST00000367797
15
ENSE00000814496
chr1:
169500260-169500024
237
FA5_HUMAN
1658-1736
79
0
-
-
1.16
ENST00000367797
16
ENSE00001376235
chr1:
169499056-169498846
211
FA5_HUMAN
1737-1807
71
0
-
-
1.17
ENST00000367797
17
ENSE00001388919
chr1:
169497332-169497153
180
FA5_HUMAN
1807-1867
61
0
-
-
1.18
ENST00000367797
18
ENSE00001367181
chr1:
169495255-169495139
117
FA5_HUMAN
1867-1906
40
0
-
-
1.19
ENST00000367797
19
ENSE00001168291
chr1:
169494146-169494075
72
FA5_HUMAN
1906-1930
25
0
-
-
1.20
ENST00000367797
20
ENSE00001168281
chr1:
169493142-169493039
104
FA5_HUMAN
1930-1964
35
0
-
-
1.21
ENST00000367797
21
ENSE00000814502
chr1:
169492590-169492435
156
FA5_HUMAN
1965-2016
52
0
-
-
1.22
ENST00000367797
22
ENSE00000814503
chr1:
169489902-169489758
145
FA5_HUMAN
2017-2065
49
0
-
-
1.23
ENST00000367797
23
ENSE00001168273
chr1:
169487801-169487650
152
FA5_HUMAN
2065-2115
51
0
-
-
1.24b
ENST00000367797
24b
ENSE00000814505
chr1:
169484864-169484682
183
FA5_HUMAN
2116-2176
61
0
-
-
1.25
ENST00000367797
25
ENSE00001627321
chr1:
169483697-169483404
294
FA5_HUMAN
2177-2224
48
0
-
-
[
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SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
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Sorry, no Info available
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CATH Domains
(0, 0)
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all CATH domains
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Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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