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5DO4
Asym. Unit
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Asym.Unit (72 KB)
Biol.Unit 1 (65 KB)
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(1)
Title
:
THROMBIN-RNA APTAMER COMPLEX
Authors
:
P. S. Pallan, M. Egli
Date
:
10 Sep 15 (Deposition) - 14 Sep 16 (Release) - 26 Oct 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.86
Chains
:
Asym. Unit : A,H,L
Biol. Unit 1: A,H,L (1x)
Keywords
:
Thrombin-Rna Aptamer, Phosphorodithioate Rna, Ps2-Rna, Ps2 Linkage, Hydrolase-Rna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. D. Abeydeera, M. Egli, N. Cox, K. Mercier, J. N. Conde, P. S. Pallan, D. M. Mizurini, M. Sierant, F. E. Hibti, T. Hassell, T. Wang, F. W. Liu, H. M. Liu, C. Martinez, A. K. Sood, T. P. Lybrand, C. Frydman, R. Q. Monteiro, R. H. Gomer, B. Nawrot, X. Yang
Evoking Picomolar Binding In Rna By A Single Phosphorodithioate Linkage.
Nucleic Acids Res. V. 44 8052 2016
[
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Hetero Components
(11, 22)
Info
All Hetero Components
01a: D-PHENYLALANYL-N-[(2S,3S)-6-{[AMIN... (0G6a)
02a: ADENOSINE-5'-(DITHIO)PHOSPHATE (ADSa)
03a: CALCIUM ION (CAa)
04a: 2'-DEOXY-2'-FLUOROCYTIDINE 5'-(DIH... (CFZa)
04b: 2'-DEOXY-2'-FLUOROCYTIDINE 5'-(DIH... (CFZb)
04c: 2'-DEOXY-2'-FLUOROCYTIDINE 5'-(DIH... (CFZc)
04d: 2'-DEOXY-2'-FLUOROCYTIDINE 5'-(DIH... (CFZd)
04e: 2'-DEOXY-2'-FLUOROCYTIDINE 5'-(DIH... (CFZe)
04f: 2'-DEOXY-2'-FLUOROCYTIDINE 5'-(DIH... (CFZf)
05a: 1,2-ETHANEDIOL (EDOa)
05b: 1,2-ETHANEDIOL (EDOb)
05c: 1,2-ETHANEDIOL (EDOc)
05d: 1,2-ETHANEDIOL (EDOd)
06a: GLYCEROL (GOLa)
06b: GLYCEROL (GOLb)
07a: MAGNESIUM ION (MGa)
08a: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDa)
09a: N-ACETYL-D-GLUCOSAMINE (NAGa)
10a: 2'-DEOXY-2'-FLUOROURIDINE 5'-(DIHY... (UFTa)
10b: 2'-DEOXY-2'-FLUOROURIDINE 5'-(DIHY... (UFTb)
11a: 2'-METHYLSELENYL-2'-DEOXYURIDINE-5... (UMSa)
11b: 2'-METHYLSELENYL-2'-DEOXYURIDINE-5... (UMSb)
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
ADS
1
Mod. Nucleotide
ADENOSINE-5'-(DITHIO)PHOSPHATE
3
CA
1
Ligand/Ion
CALCIUM ION
4
CFZ
6
Mod. Nucleotide
2'-DEOXY-2'-FLUOROCYTIDINE 5'-(DIHYDROGEN PHOSPHATE)
5
EDO
4
Ligand/Ion
1,2-ETHANEDIOL
6
GOL
2
Ligand/Ion
GLYCEROL
7
MG
1
Ligand/Ion
MAGNESIUM ION
8
MRD
1
Ligand/Ion
(4R)-2-METHYLPENTANE-2,4-DIOL
9
NAG
1
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
10
UFT
2
Mod. Nucleotide
2'-DEOXY-2'-FLUOROURIDINE 5'-(DIHYDROGEN PHOSPHATE)
11
UMS
2
Mod. Nucleotide
2'-METHYLSELENYL-2'-DEOXYURIDINE-5'-PHOSPHATE
[
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]
Sites
(18, 18)
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
16: AD7 (SOFTWARE)
17: AD8 (SOFTWARE)
18: AD9 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS H:43 , TYR H:47 , LEU H:96 , ASP H:199 , ALA H:200 , GLY H:203 , SER H:205 , SER H:226 , TRP H:227 , GLY H:228 , GLY H:230 , GLY H:238 , HOH H:407 , HOH H:415 , HOH H:435 , HOH H:436 , HOH H:491 , HOH H:503
binding site for residue 0G6 H 301
02
AC2
SOFTWARE
ILE H:78 , MET H:80 , TYR H:134
binding site for residue EDO H 303
03
AC3
SOFTWARE
LYS H:212 , ASN H:217 , HOH H:446 , LEU L:20
binding site for residue EDO H 304
04
AC4
SOFTWARE
HOH H:414 , HOH H:469 , HOH H:513
binding site for residue EDO H 305
05
AC5
SOFTWARE
A A:15 , ADS A:18 , ARG H:245
binding site for residue EDO H 306
06
AC6
SOFTWARE
ARG H:178 , GLN H:251 , HOH H:434 , GLU L:6
binding site for residue GOL H 307
07
AC7
SOFTWARE
GLN H:24 , ILE H:78 , GLU H:124 , PHE H:215
binding site for residue GOL H 308
08
AC8
SOFTWARE
ARG H:233 , LYS H:236 , HOH H:405 , HOH H:442 , HOH H:463 , HOH H:504
binding site for residue CA H 309
09
AC9
SOFTWARE
A A:14 , A A:15 , HOH A:201 , HOH A:204 , HOH A:207 , LEU H:130 , ALA H:132 , VAL H:168 , GLU H:169 , ARG H:170 , PHE H:186 , HOH H:416
binding site for residue MRD A 101
10
AD1
SOFTWARE
A A:8 , A A:9 , HOH A:202 , HOH A:210 , HOH A:211 , HOH A:215
binding site for residue MG A 102
11
AD2
SOFTWARE
ASN H:53 , HOH H:401
binding site for Mono-Saccharide NAG H 302 bound to ASN H 53
12
AD3
SOFTWARE
G A:10 , G A:13 , A A:15 , G A:16 , CFZ A:19 , HOH A:205 , HOH A:214 , ASP H:183 , HOH H:424
binding site for residues CFZ A 11 and UMS A 12
13
AD4
SOFTWARE
A A:5 , CFZ A:6 , A A:7 , A A:8 , G A:16 , CFZ A:19 , UFT A:20 , HOH A:203 , HOH A:206 , HOH A:212 , ARG H:73 , ARG H:123 , EDO H:306
binding site for residues UFT A 17 and ADS A 18
14
AD5
SOFTWARE
A A:5 , CFZ A:6 , A A:7 , A A:8 , G A:10 , CFZ A:11 , G A:16 , UFT A:17 , UFT A:20 , HOH A:206 , ARG H:123 , EDO H:306
binding site for residues ADS A 18 and CFZ A 19
15
AD6
SOFTWARE
A A:7 , A A:8 , A A:9 , G A:10 , CFZ A:11 , G A:16 , UFT A:17 , ADS A:18 , UMS A:21
binding site for residues CFZ A 19 and UFT A 20
16
AD7
SOFTWARE
A A:8 , A A:9 , G A:10 , ADS A:18 , CFZ A:19 , A A:22
binding site for residues UFT A 20 and UMS A 21
17
AD8
SOFTWARE
G A:2 , G A:3 , A A:4 , A A:22 , CFZ A:25
binding site for residues CFZ A 23 and CFZ A 24
18
AD9
SOFTWARE
G A:1 , G A:2 , G A:3 , CFZ A:23
binding site for residues CFZ A 24 and CFZ A 25
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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Exons
(0, 0)
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SCOP Domains
(0, 0)
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CATH Domains
(0, 0)
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Pfam Domains
(0, 0)
Info
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Sorry, no Info available
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Asymmetric Unit 1
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