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Getting 'Biological Unit' information from database.
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4DIH
Biol. Unit 1
Info
Asym.Unit (65 KB)
Biol.Unit 1 (60 KB)
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(1)
Title
:
X-RAY STRUCTURE OF THE COMPLEX BETWEEN HUMAN ALPHA THROMBIN AND THROMBIN BINDING APTAMER IN THE PRESENCE OF SODIUM IONS
Authors
:
I. Russo Krauss, A. Merlino, L. Mazzarella, F. Sica
Date
:
31 Jan 12 (Deposition) - 18 Jul 12 (Release) - 26 Sep 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : D,H,L
Biol. Unit 1: D,H,L (1x)
Keywords
:
Protein-Dna Complex, Serine Protease, Blood Coagulation, Aptamer, Hydrolase-Hydrolase Inhibitor-Dna Complex, Serine Protease Fold, Dna Aptamer, Blood, G-Quadruplex
(Keyword Search:
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Reference
:
I. Russo Krauss, A. Merlino, A. Randazzo, E. Novellino, L. Mazzarella, F. Sica
High-Resolution Structures Of Two Complexes Between Thrombi And Thrombin-Binding Aptamer Shed Light On The Role Of Cations In The Aptamer Inhibitory Activity.
Nucleic Acids Res. V. 40 8119 2012
(for further references see the
PDB file header
)
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Hetero Components
(2, 2)
Info
All Hetero Components
1a: D-PHENYLALANYL-N-[(2S,3S)-6-{[AMIN... (0G6a)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
4a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
5a: ZINC ION (ZNa)
5b: ZINC ION (ZNb)
5c: ZINC ION (ZNc)
View:
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Label:
No.
Name
Count
Type
Full Name
1
0G6
1
Ligand/Ion
D-PHENYLALANYL-N-[(2S,3S)-6-{[AMINO(IMINIO)METHYL]AMINO}-1-CHLORO-2-HYDROXYHEXAN-3-YL]-L-PROLINAMIDE
2
CL
-1
Ligand/Ion
CHLORIDE ION
3
NA
-1
Ligand/Ion
SODIUM ION
4
NAG
1
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
5
ZN
-1
Ligand/Ion
ZINC ION
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Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS H:119 , ASP H:222 , ASP L:1A , HOH L:203
BINDING SITE FOR RESIDUE ZN L 101
2
AC2
SOFTWARE
HIS H:57 , TYR H:60A , TRP H:60D , LEU H:99 , ILE H:174 , ASP H:189 , ALA H:190 , GLY H:193 , SER H:195 , SER H:214 , TRP H:215 , GLY H:216 , GLY H:219 , GLY H:226 , HOH H:407 , HOH H:417 , HOH H:433 , HOH H:436 , HOH H:455 , HOH H:526
BINDING SITE FOR RESIDUE 0G6 H 301
3
AC3
SOFTWARE
ASN H:60G
BINDING SITE FOR RESIDUE NAG H 302
4
AC4
SOFTWARE
ARG H:221 , LYS H:224 , HOH H:428 , HOH H:429 , HOH H:437 , HOH H:456
BINDING SITE FOR RESIDUE NA H 303
5
AC5
SOFTWARE
ASP H:60E , ASP H:125 , CL H:306 , CL H:307
BINDING SITE FOR RESIDUE ZN H 304
6
AC6
SOFTWARE
GLU H:86 , HOH H:402 , HOH H:403 , HOH H:523
BINDING SITE FOR RESIDUE ZN H 305
7
AC7
SOFTWARE
TYR H:208 , ZN H:304
BINDING SITE FOR RESIDUE CL H 306
8
AC8
SOFTWARE
ZN H:304 , HOH H:413
BINDING SITE FOR RESIDUE CL H 307
9
AC9
SOFTWARE
DG D:1 , DG D:2 , DG D:5 , DG D:6 , DG D:10 , DG D:11 , DG D:14 , DG D:15
BINDING SITE FOR RESIDUE NA D 101
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SAPs(SNPs)/Variants
(8, 8)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_006714 (M32T, chain H, )
2: VAR_011782 (P37T, chain H, )
3: VAR_006715 (R67C, chain H, )
4: VAR_006716 (R73H, chain H, )
5: VAR_006717 (R101W, chain H, )
6: VAR_006718 (E146A, chain H, )
7: VAR_068913 (E164Q, chain H, )
8: VAR_006719 (G226V, chain H, )
View:
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Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_006714
M
380
T
THRB_HUMAN
Disease (FA2D)
---
H
M
32
T
2
UniProt
VAR_011782
P
386
T
THRB_HUMAN
Polymorphism
5897
H
P
37
T
3
UniProt
VAR_006715
R
425
C
THRB_HUMAN
Disease (FA2D)
---
H
R
67
C
4
UniProt
VAR_006716
R
431
H
THRB_HUMAN
Disease (FA2D)
---
H
R
73
H
5
UniProt
VAR_006717
R
461
W
THRB_HUMAN
Disease (FA2D)
---
H
R
101
W
6
UniProt
VAR_006718
E
509
A
THRB_HUMAN
Disease (FA2D)
---
H
E
146
A
7
UniProt
VAR_068913
E
532
Q
THRB_HUMAN
Polymorphism
---
H
E
164
Q
8
UniProt
VAR_006719
G
601
V
THRB_HUMAN
Disease (FA2D)
---
H
G
226
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(3, 3)
Info
All PROSITE Patterns/Profiles
1: TRYPSIN_DOM (H:16-243)
2: TRYPSIN_HIS (H:53-58)
3: TRYPSIN_SER (H:189-200)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TRYPSIN_DOM
PS50240
Serine proteases, trypsin domain profile.
THRB_HUMAN
364-618
1
H:16-243
2
TRYPSIN_HIS
PS00134
Serine proteases, trypsin family, histidine active site.
THRB_HUMAN
402-407
1
H:53-58
3
TRYPSIN_SER
PS00135
Serine proteases, trypsin family, serine active site.
THRB_HUMAN
562-573
1
H:189-200
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
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CATH Domains
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Pfam Domains
(0, 0)
Info
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Chain D
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Chain L
Asymmetric Unit 1
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Asym.Unit (65 KB)
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