Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3ODU

The 2.5 A structure of the CXCR4 chemokine receptor in complex with small molecule antagonist IT1t

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003796	molecular_function	lysozyme activity
A	0003824	molecular_function	catalytic activity
A	0004930	molecular_function	G protein-coupled receptor activity
A	0007186	biological_process	G protein-coupled receptor signaling pathway
A	0009253	biological_process	peptidoglycan catabolic process
A	0016020	cellular_component	membrane
A	0016787	molecular_function	hydrolase activity
A	0016798	molecular_function	hydrolase activity, acting on glycosyl bonds
A	0016998	biological_process	cell wall macromolecule catabolic process
A	0019955	molecular_function	cytokine binding
A	0030430	cellular_component	host cell cytoplasm
A	0031640	biological_process	killing of cells of another organism
A	0042742	biological_process	defense response to bacterium
A	0044659	biological_process	viral release from host cell by cytolysis
B	0003796	molecular_function	lysozyme activity
B	0003824	molecular_function	catalytic activity
B	0004930	molecular_function	G protein-coupled receptor activity
B	0007186	biological_process	G protein-coupled receptor signaling pathway
B	0009253	biological_process	peptidoglycan catabolic process
B	0016020	cellular_component	membrane
B	0016787	molecular_function	hydrolase activity
B	0016798	molecular_function	hydrolase activity, acting on glycosyl bonds
B	0016998	biological_process	cell wall macromolecule catabolic process
B	0019955	molecular_function	cytokine binding
B	0030430	cellular_component	host cell cytoplasm
B	0031640	biological_process	killing of cells of another organism
B	0042742	biological_process	defense response to bacterium
B	0044659	biological_process	viral release from host cell by cytolysis

Functional Information from PDB Data

site_id	AC1
Number of Residues	10
Details	BINDING SITE FOR RESIDUE ITD A 1500

Chain	Residue
A	TRP94
A	HOH1720
A	ASP97
A	TYR116
A	ARG183
A	ILE185
A	CYS186
A	ASP187
A	GLU288
A	HOH1629

site_id	AC2
Number of Residues	9
Details	BINDING SITE FOR RESIDUE ITD B 1500

Chain	Residue
B	TRP94
B	ASP97
B	TYR116
B	ARG183
B	CYS186
B	ASP187
B	GLU288
B	HOH1642
B	HOH1685

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE OLC A 1600

Chain	Residue
A	PHE104
A	PHE107
A	LEU108
B	PHE107

site_id	AC4
Number of Residues	9
Details	BINDING SITE FOR RESIDUE OLC B 1601

Chain	Residue
B	THR51
B	LEU58
B	VAL59
B	VAL62
B	PRO299
B	ILE300
B	TYR302
B	ALA303
B	HOH1751

site_id	AC5
Number of Residues	1
Details	BINDING SITE FOR RESIDUE OLC B 1602

Chain	Residue
B	ILE270

site_id	AC6
Number of Residues	9
Details	BINDING SITE FOR RESIDUE OLC A 1603

Chain	Residue
A	GLN200
A	PHE201
A	ILE204
A	ILE209
A	ASP262
A	SER263
A	LEU266
A	HIS281
B	VAL198

site_id	AC7
Number of Residues	9
Details	BINDING SITE FOR RESIDUE OLC A 1604

Chain	Residue
A	LEU120
A	VAL124
A	HIS203
A	ILE204
A	GLY207
A	ILE209
A	PHE248
A	TYR256
A	SER260

site_id	AC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE OLA B 1605

Chain	Residue
B	ILE39
B	THR43
B	SER46
B	TYR103

site_id	AC9
Number of Residues	9
Details	BINDING SITE FOR RESIDUE OLA B 1606

Chain	Residue
A	VAL198
B	VAL196
B	GLN200
B	PHE201
B	ILE204
B	ILE209
B	ASP262
B	SER263
B	LEU266

site_id	BC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE OLA B 1607

Chain	Residue
B	ARG70
B	LEU78
B	HIS79
B	TYR157
B	TRP161
B	LEU165

site_id	BC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE OLA B 1608

Chain	Residue
B	ALA250
B	CYS251
B	LEU290

site_id	BC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE OLA B 1609

Chain	Residue
B	LEU120
B	HIS203
B	ILE204
B	LEU208
B	TYR256
B	SER260

site_id	BC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE OLA A 1610

Chain	Residue
A	ALA100
A	TYR103

Functional Information from PROSITE/UniProt

site_id	PS00237
Number of Residues	17
Details	G_PROTEIN_RECEP_F1_1 G-protein coupled receptors family 1 signature. SSVwILAFISLDRYLaI

Chain	Residue	Details
A	SER122-ILE138

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	Active site: {"description":"Proton donor/acceptor","evidences":[{"source":"HAMAP-Rule","id":"MF_04110","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"3382407","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"7831309","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8266098","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	2
Details	Active site: {"description":"Proton donor/acceptor","evidences":[{"source":"HAMAP-Rule","id":"MF_04110","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"1892846","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"3382407","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"7831309","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8266098","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"8266098","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"7831309","evidenceCode":"ECO:0000303"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	48
Details	Transmembrane: {"description":"Helical; Name=1","evidences":[{"source":"PubMed","id":"20929726","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	72
Details	Topological domain: {"description":"Cytoplasmic","evidences":[{"source":"PubMed","id":"20929726","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	42
Details	Transmembrane: {"description":"Helical; Name=2","evidences":[{"source":"PubMed","id":"20929726","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	100
Details	Topological domain: {"description":"Extracellular","evidences":[{"source":"PubMed","id":"20929726","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	38
Details	Transmembrane: {"description":"Helical; Name=3","evidences":[{"source":"PubMed","id":"20929726","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	38
Details	Transmembrane: {"description":"Helical; Name=4","evidences":[{"source":"PubMed","id":"20929726","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	40
Details	Transmembrane: {"description":"Helical; Name=5","evidences":[{"source":"PubMed","id":"20929726","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	38
Details	Transmembrane: {"description":"Helical; Name=6","evidences":[{"source":"PubMed","id":"20929726","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	38
Details	Transmembrane: {"description":"Helical; Name=7","evidences":[{"source":"PubMed","id":"20929726","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI14
Number of Residues	6
Details	Region: {"description":"Chemokine binding","evidences":[{"source":"PubMed","id":"20929726","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"10825158","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI15
Number of Residues	8
Details	Region: {"description":"Chemokine binding"}

Chain

Residue

Details

site_id	SWS_FT_FI16
Number of Residues	24
Details	Region: {"description":"Involved in dimerization; when bound to chemokine"}

Chain

Residue

Details

site_id	SWS_FT_FI17
Number of Residues	8
Details	Region: {"description":"Chemokine binding, important for signaling and HIV-1 coreceptor activity"}

Chain

Residue

Details

site_id	SWS_FT_FI18
Number of Residues	42
Details	Region: {"description":"Involved in dimerization"}

Chain

Residue

Details

site_id	SWS_FT_FI19
Number of Residues	4
Details	Motif: {"description":"Important for signaling"}

Chain

Residue

Details

site_id	SWS_FT_FI20
Number of Residues	2
Details	Site: {"description":"Chemokine binding"}

Chain

Residue

Details

site_id	SWS_FT_FI21
Number of Residues	2
Details	Site: {"description":"Chemokine binding","evidences":[{"source":"PubMed","id":"20929726","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"10825158","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI22
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18669648","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI23
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine; by PKC and GRK6","evidences":[{"source":"PubMed","id":"19116316","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20048153","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI24
Number of Residues	2
Details	Glycosylation: {"description":"N-linked (GlcNAc...) asparagine","evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	2
Details	M-CSA 921

Chain	Residue	Details
A	GLU1011	proton shuttle (general acid/base)
A	ASP1020	covalent catalysis

site_id	MCSA2
Number of Residues	2
Details	M-CSA 921

Chain	Residue	Details
B	GLU1011	proton shuttle (general acid/base)
B	ASP1020	covalent catalysis

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)