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3DD2
Biol. Unit 1
Info
Asym.Unit (74 KB)
Biol.Unit 1 (67 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF AN RNA APTAMER BOUND TO HUMAN THROMBIN
Authors
:
S. B. Long, B. A. Sullenger
Date
:
04 Jun 08 (Deposition) - 11 Nov 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : B,H,L
Biol. Unit 1: B,H,L (1x)
Keywords
:
Thrombin, Aptamer, Rna, Dna, Heparin, Exosite, Protease, Serine Protease, Hydrolase-Hydrolase Inhibitor-Rna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. B. Long, M. B. Long, R. R. White, B. A. Sullenger
Crystal Structure Of An Rna Aptamer Bound To Thrombin.
Rna V. 14 2504 2008
[
close entry info
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Hetero Components
(6, 21)
Info
All Hetero Components
1a: D-PHENYLALANYL-N-[(2S,3S)-6-{[AMIN... (0G6a)
2a: ACETIC ACID (ACYa)
2b: ACETIC ACID (ACYb)
2c: ACETIC ACID (ACYc)
2d: ACETIC ACID (ACYd)
2e: ACETIC ACID (ACYe)
2f: ACETIC ACID (ACYf)
3a: 4-AMINO-1-(2-DEOXY-2-FLUORO-5-O-PH... (CFLa)
3b: 4-AMINO-1-(2-DEOXY-2-FLUORO-5-O-PH... (CFLb)
3c: 4-AMINO-1-(2-DEOXY-2-FLUORO-5-O-PH... (CFLc)
3d: 4-AMINO-1-(2-DEOXY-2-FLUORO-5-O-PH... (CFLd)
3e: 4-AMINO-1-(2-DEOXY-2-FLUORO-5-O-PH... (CFLe)
3f: 4-AMINO-1-(2-DEOXY-2-FLUORO-5-O-PH... (CFLf)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
5a: HEXAETHYLENE GLYCOL (P6Ga)
6a: DI(HYDROXYETHYL)ETHER (PEGa)
6b: DI(HYDROXYETHYL)ETHER (PEGb)
6c: DI(HYDROXYETHYL)ETHER (PEGc)
7a: 2'-DEOXY-2'-FLUOROURIDINE 5'-(DIHY... (UFTa)
7b: 2'-DEOXY-2'-FLUOROURIDINE 5'-(DIHY... (UFTb)
7c: 2'-DEOXY-2'-FLUOROURIDINE 5'-(DIHY... (UFTc)
7d: 2'-DEOXY-2'-FLUOROURIDINE 5'-(DIHY... (UFTd)
View:
Select:
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
ACY
6
Ligand/Ion
ACETIC ACID
3
CFL
6
Mod. Nucleotide
4-AMINO-1-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)PYRIMIDIN-2(1H)-ONE
4
MG
-1
Ligand/Ion
MAGNESIUM ION
5
P6G
1
Ligand/Ion
HEXAETHYLENE GLYCOL
6
PEG
3
Ligand/Ion
DI(HYDROXYETHYL)ETHER
7
UFT
4
Mod. Nucleotide
2'-DEOXY-2'-FLUOROURIDINE 5'-(DIHYDROGEN PHOSPHATE)
[
close Hetero Component info
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Sites
(13, 13)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
A B:14 , GLN H:131 , ALA H:132 , TYR H:134 , ILE L:14K , ASP L:14L , HOH L:209
BINDING SITE FOR RESIDUE PEG L 305
02
AC2
SOFTWARE
A B:7 , A B:8 , A B:9 , HOH B:1003 , HOH B:1006 , HOH B:1009 , HOH B:1018
BINDING SITE FOR RESIDUE MG B1000
03
AC3
SOFTWARE
HIS H:57 , TYR H:60A , LEU H:99 , 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:247 , HOH H:248 , HOH H:249 , HOH H:250 , HOH H:1024
BINDING SITE FOR RESIDUE 0G6 H 1
04
AC4
SOFTWARE
A B:4 , A B:5 , CFL B:23
BINDING SITE FOR RESIDUE ACY B 151
05
AC5
SOFTWARE
G B:2 , G B:3 , HOH B:1017
BINDING SITE FOR RESIDUE ACY B 152
06
AC6
SOFTWARE
G B:3 , CFL B:23 , CFL B:24
BINDING SITE FOR RESIDUE PEG B 103
07
AC7
SOFTWARE
CFL B:11 , CFL B:19 , UFT B:20 , HOH B:1021 , HOH B:1044 , ALA H:149A
BINDING SITE FOR RESIDUE PEG B 104
08
AC8
SOFTWARE
ARG H:221 , LYS H:224 , HOH H:1012 , HOH H:1032 , HOH H:1037 , HOH H:1047
BINDING SITE FOR RESIDUE MG H1002
09
AC9
SOFTWARE
GLN H:38 , LEU H:65 , TYR H:76 , ILE H:82 , SER H:129B , LEU H:129C , PRO H:204 , PHE H:204A , HOH H:1127 , HOH H:1135 , HOH H:1137
BINDING SITE FOR RESIDUE P6G H1003
10
BC1
SOFTWARE
ASN H:60G , ACY H:1007
BINDING SITE FOR RESIDUE ACY H1004
11
BC2
SOFTWARE
GLY H:19 , HOH H:1153
BINDING SITE FOR RESIDUE ACY H1005
12
BC3
SOFTWARE
PHE H:114 , PRO H:120 , ARG H:173 , HOH H:1062 , HOH H:1087 , ASP L:1A , ALA L:1B
BINDING SITE FOR RESIDUE ACY H1006
13
BC4
SOFTWARE
ASN H:60G , ACY H:1004
BINDING SITE FOR RESIDUE ACY H1007
[
close Site info
]
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:
Select:
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)
[
close SNP/Variant info
]
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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Label:
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)
Info
All Exons
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All Exon Boundaries
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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
(0, 0)
Info
All SCOP Domains
View:
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Label:
Sorry, no Info available
[
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_3dd2H02 (H:28-120,H:233-245)
1b: CATH_3dd2H01 (H:16-27,H:121-232)
View:
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Classes
(
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(
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Architectures
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(
)
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)
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)
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(
)
(
)
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
3dd2H02
H:28-120,H:233-245
1b
3dd2H01
H:16-27,H:121-232
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Atom Selection
(currently selected atoms:
all
)
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Nucleic
Backbone
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Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain B
Chain H
Chain L
Asymmetric Unit 1
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