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3DD2
Asym. Unit
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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
]
Hetero Components
(7, 23)
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
2
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
]
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 not available)
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:
Select:
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
[
close PROSITE info
]
Exons
(7, 8)
Info
All Exons
Exon 1.8 (- | L:1D-1A)
Exon 1.9 (H:16-29 | L:1A-14L)
Exon 1.10 (H:29-75 | -)
Exon 1.11b (H:75-129B | -)
Exon 1.12 (H:129B-184 | -)
Exon 1.13 (H:184-202 | -)
Exon 1.14c (H:203-246 (gaps) | -)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.7b/1.8
2: Boundary 1.8/1.9
3: Boundary 1.9/1.10
4: Boundary 1.10/1.11b
5: Boundary 1.11b/1.12
6: Boundary 1.12/1.13
7: Boundary 1.13/1.14c
8: Boundary 1.14c/-
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
ENST00000311907
1a
ENSE00001931088
chr11:
46740730-46740864
135
THRB_HUMAN
1-27
27
0
-
-
1.2a
ENST00000311907
2a
ENSE00001181543
chr11:
46741252-46741412
161
THRB_HUMAN
27-80
54
0
-
-
1.3
ENST00000311907
3
ENSE00001181538
chr11:
46742073-46742097
25
THRB_HUMAN
81-89
9
0
-
-
1.4
ENST00000311907
4
ENSE00001181532
chr11:
46742340-46742390
51
THRB_HUMAN
89-106
18
0
-
-
1.6a
ENST00000311907
6a
ENSE00001181527
chr11:
46744730-46744835
106
THRB_HUMAN
106-141
36
0
-
-
1.6c
ENST00000311907
6c
ENSE00001181524
chr11:
46744932-46745068
137
THRB_HUMAN
141-187
47
0
-
-
1.7b
ENST00000311907
7b
ENSE00001688723
chr11:
46747409-46747723
315
THRB_HUMAN
187-292
106
0
-
-
1.8
ENST00000311907
8
ENSE00002179953
chr11:
46748048-46748176
129
THRB_HUMAN
292-335
44
1
-
L:1D-1A
-
4
1.9
ENST00000311907
9
ENSE00001770269
chr11:
46748261-46748387
127
THRB_HUMAN
335-377
43
2
H:16-29
L:1A-14L
14
27
1.10
ENST00000311907
10
ENSE00001650441
chr11:
46749546-46749713
168
THRB_HUMAN
377-433
57
1
H:29-75
-
57
-
1.11b
ENST00000311907
11b
ENSE00001657931
chr11:
46750214-46750387
174
THRB_HUMAN
433-491
59
1
H:75-129B
-
59
-
1.12
ENST00000311907
12
ENSE00001646362
chr11:
46750930-46751111
182
THRB_HUMAN
491-552
62
1
H:129B-184
-
62
-
1.13
ENST00000311907
13
ENSE00001680217
chr11:
46760598-46760668
71
THRB_HUMAN
552-575
24
1
H:184-202
-
24
-
1.14c
ENST00000311907
14c
ENSE00001227030
chr11:
46760815-46761056
242
THRB_HUMAN
576-622
47
1
H:203-246 (gaps)
-
47
-
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
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:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
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
3dd2H02
H:28-120,H:233-245
1b
3dd2H01
H:16-27,H:121-232
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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(currently selected atoms:
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)
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Protein & NOT PROSITE
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Chain H
Chain L
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