3DD2

Crystal structure of an RNA aptamer bound to human thrombin

Functional Information from GO Data

Chain	GOid	namespace	contents
H	0004252	molecular_function	serine-type endopeptidase activity
H	0005509	molecular_function	calcium ion binding
H	0006508	biological_process	proteolysis
H	0007596	biological_process	blood coagulation
L	0004252	molecular_function	serine-type endopeptidase activity
L	0005576	cellular_component	extracellular region
L	0006508	biological_process	proteolysis
L	0007596	biological_process	blood coagulation

Functional Information from PDB Data

site_id	AC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE PEG L 305

Chain	Residue
B	A14
H	GLN131
H	ALA132
H	TYR134
L	ILE14
L	ASP14
L	HOH209

---

site_id	AC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE MG B1000

Chain	Residue
B	A9
B	HOH1003
B	HOH1006
B	HOH1009
B	HOH1018
B	A7
B	A8

---

site_id	AC3
Number of Residues	17
Details	BINDING SITE FOR RESIDUE 0G6 H 1

Chain	Residue
H	HIS57
H	TYR60
H	LEU99
H	ASP189
H	ALA190
H	GLY193
H	SER195
H	SER214
H	TRP215
H	GLY216
H	GLY219
H	GLY226
H	HOH247
H	HOH248
H	HOH249
H	HOH250
H	HOH1024

---

site_id	AC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ACY B 151

Chain	Residue
B	A4
B	A5
B	CFL23

---

site_id	AC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ACY B 152

Chain	Residue
B	G2
B	G3
B	HOH1017

---

site_id	AC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE PEG B 103

Chain	Residue
B	G3
B	CFL23
B	CFL24

---

site_id	AC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE PEG B 104

Chain	Residue
B	CFL11
B	CFL19
B	UFT20
B	HOH1021
B	HOH1044
H	ALA149

---

site_id	AC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG H1002

Chain	Residue
H	ARG221
H	LYS224
H	HOH1012
H	HOH1032
H	HOH1037
H	HOH1047

---

site_id	AC9
Number of Residues	11
Details	BINDING SITE FOR RESIDUE P6G H1003

Chain	Residue
H	GLN38
H	LEU65
H	TYR76
H	ILE82
H	SER129
H	LEU129
H	PRO204
H	PHE204
H	HOH1127
H	HOH1135
H	HOH1137

---

site_id	BC1
Number of Residues	2
Details	BINDING SITE FOR RESIDUE ACY H1004

Chain	Residue
H	ASN60
H	ACY1007

---

site_id	BC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE ACY H1005

Chain	Residue
H	GLY19
H	HOH1153

---

site_id	BC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE ACY H1006

Chain	Residue
H	PHE114
H	PRO120
H	ARG173
H	HOH1062
H	HOH1087
L	ASP1
L	ALA1

---

site_id	BC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE ACY H1007

Chain	Residue
H	ASN60
H	ACY1004

---

Functional Information from PROSITE/UniProt

site_id	PS00134
Number of Residues	6
Details	TRYPSIN_HIS Serine proteases, trypsin family, histidine active site. LTAAHC

Chain	Residue	Details
H	LEU53-CYS58

---

site_id	PS00135
Number of Residues	12
Details	TRYPSIN_SER Serine proteases, trypsin family, serine active site. DAceGDSGGPFV

Chain	Residue	Details
H	ASP189-VAL200

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	254
Details	Domain: {"description":"Peptidase S1","evidences":[{"source":"PROSITE-ProRule","id":"PRU00274","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	22
Details	Region: {"description":"High affinity receptor-binding region which is also known as the TP508 peptide"}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	3
Details	Active site: {"description":"Charge relay system"}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	1
Details	Glycosylation: {"description":"N-linked (GlcNAc...) (complex) asparagine","evidences":[{"source":"PubMed","id":"16335952","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19139490","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19159218","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19838169","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"873923","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

Catalytic Information from CSA

site_id	CSA1
Number of Residues	2
Details	Annotated By Reference To The Literature 1a0j

Chain	Residue	Details
H	ASP102
H	HIS57

---

site_id	CSA2
Number of Residues	2
Details	Annotated By Reference To The Literature 1a0j

Chain	Residue	Details
H	SER195
H	GLY193

---

site_id	CSA3
Number of Residues	2
Details	Annotated By Reference To The Literature 1a0j

Chain	Residue	Details
H	SER195
H	GLY196

---

site_id	CSA4
Number of Residues	3
Details	Annotated By Reference To The Literature 1a0j

Chain	Residue	Details
H	ASP102
H	SER195
H	HIS57

---

site_id	CSA5
Number of Residues	4
Details	Annotated By Reference To The Literature 1a0j

Chain	Residue	Details
H	ASP102
H	SER195
H	HIS57
H	GLY196

---

site_id	CSA6
Number of Residues	4
Details	Annotated By Reference To The Literature 1a0j

Chain	Residue	Details
H	ASP102
H	SER195
H	GLY193
H	HIS57

---