Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3VPB

ArgX from Sulfolobus tokodaii complexed with LysW/Glu/ADP/Mg/Zn/Sulfate

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0003824	molecular_function	catalytic activity
A	0005524	molecular_function	ATP binding
A	0005737	cellular_component	cytoplasm
A	0006526	biological_process	L-arginine biosynthetic process
A	0008652	biological_process	amino acid biosynthetic process
A	0009085	biological_process	lysine biosynthetic process
A	0016874	molecular_function	ligase activity
A	0016879	molecular_function	ligase activity, forming carbon-nitrogen bonds
A	0036211	biological_process	protein modification process
A	0042802	molecular_function	identical protein binding
A	0043774	molecular_function	coenzyme F420-2 alpha-glutamyl ligase activity
A	0046872	molecular_function	metal ion binding
B	0000166	molecular_function	nucleotide binding
B	0003824	molecular_function	catalytic activity
B	0005524	molecular_function	ATP binding
B	0005737	cellular_component	cytoplasm
B	0006526	biological_process	L-arginine biosynthetic process
B	0008652	biological_process	amino acid biosynthetic process
B	0009085	biological_process	lysine biosynthetic process
B	0016874	molecular_function	ligase activity
B	0016879	molecular_function	ligase activity, forming carbon-nitrogen bonds
B	0036211	biological_process	protein modification process
B	0042802	molecular_function	identical protein binding
B	0043774	molecular_function	coenzyme F420-2 alpha-glutamyl ligase activity
B	0046872	molecular_function	metal ion binding
C	0000166	molecular_function	nucleotide binding
C	0003824	molecular_function	catalytic activity
C	0005524	molecular_function	ATP binding
C	0005737	cellular_component	cytoplasm
C	0006526	biological_process	L-arginine biosynthetic process
C	0008652	biological_process	amino acid biosynthetic process
C	0009085	biological_process	lysine biosynthetic process
C	0016874	molecular_function	ligase activity
C	0016879	molecular_function	ligase activity, forming carbon-nitrogen bonds
C	0036211	biological_process	protein modification process
C	0042802	molecular_function	identical protein binding
C	0043774	molecular_function	coenzyme F420-2 alpha-glutamyl ligase activity
C	0046872	molecular_function	metal ion binding
D	0000166	molecular_function	nucleotide binding
D	0003824	molecular_function	catalytic activity
D	0005524	molecular_function	ATP binding
D	0005737	cellular_component	cytoplasm
D	0006526	biological_process	L-arginine biosynthetic process
D	0008652	biological_process	amino acid biosynthetic process
D	0009085	biological_process	lysine biosynthetic process
D	0016874	molecular_function	ligase activity
D	0016879	molecular_function	ligase activity, forming carbon-nitrogen bonds
D	0036211	biological_process	protein modification process
D	0042802	molecular_function	identical protein binding
D	0043774	molecular_function	coenzyme F420-2 alpha-glutamyl ligase activity
D	0046872	molecular_function	metal ion binding
E	0006526	biological_process	L-arginine biosynthetic process
E	0008270	molecular_function	zinc ion binding
E	0008652	biological_process	amino acid biosynthetic process
E	0009085	biological_process	lysine biosynthetic process
E	0019878	biological_process	lysine biosynthetic process via aminoadipic acid
E	0046872	molecular_function	metal ion binding
F	0006526	biological_process	L-arginine biosynthetic process
F	0008270	molecular_function	zinc ion binding
F	0008652	biological_process	amino acid biosynthetic process
F	0009085	biological_process	lysine biosynthetic process
F	0019878	biological_process	lysine biosynthetic process via aminoadipic acid
F	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	26
Details	BINDING SITE FOR RESIDUE ADP A 500

Chain	Residue
A	LYS87
A	TYR169
A	ILE170
A	ASP176
A	ARG200
A	ALA201
A	ASN202
A	ASP237
A	LEU239
A	ASN249
A	GLU250
A	LYS127
A	MG502
A	ZN503
A	SO4504
A	HOH621
A	HOH624
A	HOH642
A	HOH696
A	GLY131
A	SER132
A	TRP133
A	GLY134
A	VAL137
A	GLN167
A	GLU168

site_id	AC2
Number of Residues	13
Details	BINDING SITE FOR RESIDUE GLU A 501

Chain	Residue
A	TYR190
A	ARG192
A	ASN202
A	VAL203
A	ALA204
A	GLU256
A	LYS258
A	GLY259
A	PHE260
A	SO4504
A	HOH626
A	HOH635
E	GLU56

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG A 502

Chain	Residue
A	ASP237
A	GLU250
A	ADP500
A	ZN503
A	SO4504
A	HOH642

site_id	AC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN A 503

Chain	Residue
A	GLU250
A	ASN252
A	ADP500
A	MG502
A	SO4504
A	HOH696

site_id	AC5
Number of Residues	14
Details	BINDING SITE FOR RESIDUE SO4 A 504

Chain	Residue
A	SER132
A	TRP133
A	ARG178
A	ARG192
A	ASN202
A	ASP237
A	GLU250
A	ASN252
A	ADP500
A	GLU501
A	MG502
A	ZN503
A	HOH642
E	GLU56

site_id	AC6
Number of Residues	24
Details	BINDING SITE FOR RESIDUE ADP B 500

Chain	Residue
B	LYS87
B	LYS127
B	GLY131
B	SER132
B	TRP133
B	GLY134
B	GLN167
B	GLU168
B	TYR169
B	ILE170
B	ASP176
B	ARG200
B	ALA201
B	ASN202
B	ASP237
B	ASN249
B	GLU250
B	MG502
B	ZN503
B	SO4504
B	HOH617
B	HOH621
B	HOH650
B	HOH651

site_id	AC7
Number of Residues	15
Details	BINDING SITE FOR RESIDUE GLU B 501

Chain	Residue
B	SO4504
B	HOH654
B	HOH658
B	HOH689
F	GLU56
B	ARG178
B	TYR190
B	ARG192
B	ASN202
B	VAL203
B	ALA204
B	GLU256
B	LYS258
B	GLY259
B	PHE260

site_id	AC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG B 502

Chain	Residue
B	ASP237
B	GLU250
B	ADP500
B	ZN503
B	SO4504
B	HOH650

site_id	AC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN B 503

Chain	Residue
B	GLU250
B	ASN252
B	ADP500
B	MG502
B	SO4504
B	HOH651

site_id	BC1
Number of Residues	14
Details	BINDING SITE FOR RESIDUE SO4 B 504

Chain	Residue
B	SER132
B	TRP133
B	ARG178
B	ARG192
B	ASN202
B	ASP237
B	GLU250
B	ASN252
B	ADP500
B	GLU501
B	MG502
B	ZN503
B	HOH650
F	GLU56

site_id	BC2
Number of Residues	27
Details	BINDING SITE FOR RESIDUE ADP C 500

Chain	Residue
C	LYS87
C	ILE125
C	LYS127
C	GLY131
C	SER132
C	TRP133
C	GLY134
C	ARG135
C	VAL137
C	GLN167
C	GLU168
C	TYR169
C	ILE170
C	ASP176
C	ARG200
C	ALA201
C	ASN202
C	ASP237
C	ASN249
C	GLU250
C	MG502
C	SO4503
C	HOH633
C	HOH651
C	HOH706
C	HOH709
C	HOH731

site_id	BC3
Number of Residues	12
Details	BINDING SITE FOR RESIDUE GLU C 501

Chain	Residue
C	TRP133
C	TYR190
C	ARG192
C	ASN202
C	VAL203
C	ALA204
C	GLU256
C	LYS258
C	GLY259
C	PHE260
C	SO4503
C	HOH639

site_id	BC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG C 502

Chain	Residue
C	ASP237
C	GLU250
C	ADP500
C	SO4503
C	HOH709

site_id	BC5
Number of Residues	14
Details	BINDING SITE FOR RESIDUE SO4 C 503

Chain	Residue
C	SER132
C	TRP133
C	ARG178
C	ARG192
C	ASN202
C	ASP237
C	GLU250
C	ASN252
C	ADP500
C	GLU501
C	MG502
C	HOH601
C	HOH633
C	HOH709

site_id	BC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 C 504

Chain	Residue
C	SER56
C	MET57
C	TYR58
D	SER159

site_id	BC7
Number of Residues	25
Details	BINDING SITE FOR RESIDUE ADP D 500

Chain	Residue
D	LYS87
D	ILE125
D	LYS127
D	GLY131
D	SER132
D	TRP133
D	GLY134
D	VAL137
D	GLN167
D	GLU168
D	TYR169
D	ILE170
D	ASP176
D	ARG200
D	ALA201
D	ASN202
D	ASP237
D	ASN249
D	GLU250
D	MG502
D	SO4503
D	HOH648
D	HOH654
D	HOH690
D	HOH699

site_id	BC8
Number of Residues	13
Details	BINDING SITE FOR RESIDUE GLU D 501

Chain	Residue
D	TRP133
D	TYR190
D	ARG192
D	ASN202
D	VAL203
D	ALA204
D	GLU256
D	LYS258
D	GLY259
D	PHE260
D	SO4503
D	HOH627
D	HOH680

site_id	BC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG D 502

Chain	Residue
D	ASP237
D	GLU250
D	ADP500
D	SO4503
D	HOH690

site_id	CC1
Number of Residues	14
Details	BINDING SITE FOR RESIDUE SO4 D 503

Chain	Residue
D	SER132
D	TRP133
D	ARG178
D	ARG192
D	ASN202
D	ASP237
D	GLU250
D	ASN252
D	ADP500
D	GLU501
D	MG502
D	HOH608
D	HOH654
D	HOH690

site_id	CC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 D 504

Chain	Residue
C	SER159
D	SER56
D	MET57
D	TYR58
D	HOH803

site_id	CC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN E 100

Chain	Residue
E	CYS6
E	CYS9
E	HIS27
E	CYS29

site_id	CC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN F 100

Chain	Residue
F	CYS6
F	CYS9
F	HIS27
F	CYS29

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	744
Details	Domain: {"description":"ATP-grasp","evidences":[{"source":"PROSITE-ProRule","id":"PRU00409","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	4
Details	Motif: {"description":"GF motif that is essential for ArgX substrate specificity","evidences":[{"source":"PubMed","id":"23434852","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	104
Details	Binding site: {"evidences":[{"source":"PubMed","id":"23434852","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"PubMed","id":"23434852","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	66
Details	Zinc finger: {"description":"TFIIB-type"}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	2
Details	Motif: {"description":"EDWGE"}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	8
Details	Binding site: {}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	2
Details	Modified residue: {"description":"5-glutamyl N2-ornithine; alternate","evidences":[{"evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

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