Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6ZJB

Crystal structure of human adenylate kinase 3, AK3, in complex with inhibitor Gp5A

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004017	molecular_function	AMP kinase activity
A	0005515	molecular_function	protein binding
A	0005524	molecular_function	ATP binding
A	0005739	cellular_component	mitochondrion
A	0005759	cellular_component	mitochondrial matrix
A	0006139	biological_process	nucleobase-containing compound metabolic process
A	0006172	biological_process	ADP biosynthetic process
A	0007596	biological_process	blood coagulation
A	0009117	biological_process	nucleotide metabolic process
A	0009123	biological_process	nucleoside monophosphate metabolic process
A	0009142	biological_process	nucleoside triphosphate biosynthetic process
A	0016776	molecular_function	phosphotransferase activity, phosphate group as acceptor
A	0019205	molecular_function	nucleobase-containing compound kinase activity
A	0046033	biological_process	AMP metabolic process
A	0046039	biological_process	GTP metabolic process
A	0046041	biological_process	ITP metabolic process
A	0046051	biological_process	UTP metabolic process
A	0046899	molecular_function	nucleoside triphosphate adenylate kinase activity
B	0004017	molecular_function	AMP kinase activity
B	0005515	molecular_function	protein binding
B	0005524	molecular_function	ATP binding
B	0005739	cellular_component	mitochondrion
B	0005759	cellular_component	mitochondrial matrix
B	0006139	biological_process	nucleobase-containing compound metabolic process
B	0006172	biological_process	ADP biosynthetic process
B	0007596	biological_process	blood coagulation
B	0009117	biological_process	nucleotide metabolic process
B	0009123	biological_process	nucleoside monophosphate metabolic process
B	0009142	biological_process	nucleoside triphosphate biosynthetic process
B	0016776	molecular_function	phosphotransferase activity, phosphate group as acceptor
B	0019205	molecular_function	nucleobase-containing compound kinase activity
B	0046033	biological_process	AMP metabolic process
B	0046039	biological_process	GTP metabolic process
B	0046041	biological_process	ITP metabolic process
B	0046051	biological_process	UTP metabolic process
B	0046899	molecular_function	nucleoside triphosphate adenylate kinase activity
C	0004017	molecular_function	AMP kinase activity
C	0005515	molecular_function	protein binding
C	0005524	molecular_function	ATP binding
C	0005739	cellular_component	mitochondrion
C	0005759	cellular_component	mitochondrial matrix
C	0006139	biological_process	nucleobase-containing compound metabolic process
C	0006172	biological_process	ADP biosynthetic process
C	0007596	biological_process	blood coagulation
C	0009117	biological_process	nucleotide metabolic process
C	0009123	biological_process	nucleoside monophosphate metabolic process
C	0009142	biological_process	nucleoside triphosphate biosynthetic process
C	0016776	molecular_function	phosphotransferase activity, phosphate group as acceptor
C	0019205	molecular_function	nucleobase-containing compound kinase activity
C	0046033	biological_process	AMP metabolic process
C	0046039	biological_process	GTP metabolic process
C	0046041	biological_process	ITP metabolic process
C	0046051	biological_process	UTP metabolic process
C	0046899	molecular_function	nucleoside triphosphate adenylate kinase activity
D	0004017	molecular_function	AMP kinase activity
D	0005515	molecular_function	protein binding
D	0005524	molecular_function	ATP binding
D	0005739	cellular_component	mitochondrion
D	0005759	cellular_component	mitochondrial matrix
D	0006139	biological_process	nucleobase-containing compound metabolic process
D	0006172	biological_process	ADP biosynthetic process
D	0007596	biological_process	blood coagulation
D	0009117	biological_process	nucleotide metabolic process
D	0009123	biological_process	nucleoside monophosphate metabolic process
D	0009142	biological_process	nucleoside triphosphate biosynthetic process
D	0016776	molecular_function	phosphotransferase activity, phosphate group as acceptor
D	0019205	molecular_function	nucleobase-containing compound kinase activity
D	0046033	biological_process	AMP metabolic process
D	0046039	biological_process	GTP metabolic process
D	0046041	biological_process	ITP metabolic process
D	0046051	biological_process	UTP metabolic process
D	0046899	molecular_function	nucleoside triphosphate adenylate kinase activity
E	0004017	molecular_function	AMP kinase activity
E	0005515	molecular_function	protein binding
E	0005524	molecular_function	ATP binding
E	0005739	cellular_component	mitochondrion
E	0005759	cellular_component	mitochondrial matrix
E	0006139	biological_process	nucleobase-containing compound metabolic process
E	0006172	biological_process	ADP biosynthetic process
E	0007596	biological_process	blood coagulation
E	0009117	biological_process	nucleotide metabolic process
E	0009123	biological_process	nucleoside monophosphate metabolic process
E	0009142	biological_process	nucleoside triphosphate biosynthetic process
E	0016776	molecular_function	phosphotransferase activity, phosphate group as acceptor
E	0019205	molecular_function	nucleobase-containing compound kinase activity
E	0046033	biological_process	AMP metabolic process
E	0046039	biological_process	GTP metabolic process
E	0046041	biological_process	ITP metabolic process
E	0046051	biological_process	UTP metabolic process
E	0046899	molecular_function	nucleoside triphosphate adenylate kinase activity
F	0004017	molecular_function	AMP kinase activity
F	0005515	molecular_function	protein binding
F	0005524	molecular_function	ATP binding
F	0005739	cellular_component	mitochondrion
F	0005759	cellular_component	mitochondrial matrix
F	0006139	biological_process	nucleobase-containing compound metabolic process
F	0006172	biological_process	ADP biosynthetic process
F	0007596	biological_process	blood coagulation
F	0009117	biological_process	nucleotide metabolic process
F	0009123	biological_process	nucleoside monophosphate metabolic process
F	0009142	biological_process	nucleoside triphosphate biosynthetic process
F	0016776	molecular_function	phosphotransferase activity, phosphate group as acceptor
F	0019205	molecular_function	nucleobase-containing compound kinase activity
F	0046033	biological_process	AMP metabolic process
F	0046039	biological_process	GTP metabolic process
F	0046041	biological_process	ITP metabolic process
F	0046051	biological_process	UTP metabolic process
F	0046899	molecular_function	nucleoside triphosphate adenylate kinase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	44
Details	binding site for residue G5P A 301

Chain	Residue
A	PRO16
A	ARG43
A	ILE60
A	LYS64
A	LEU65
A	ILE66
A	MET71
A	GLY91
A	PHE92
A	ARG94
A	GLN98
A	GLY17
A	ARG124
A	ARG128
A	VAL137
A	TYR138
A	ASN139
A	GLU141
A	PHE142
A	ARG161
A	ARG172
A	GLU200
A	SER18
A	THR201
A	MG302
A	HOH411
A	HOH413
A	HOH415
A	HOH416
A	HOH421
A	HOH436
A	HOH447
A	HOH457
A	GLY19
A	HOH461
A	HOH463
A	HOH468
A	HOH471
A	HOH493
A	LYS20
A	GLY21
A	THR22
A	SER38
A	LEU42

site_id	AC2
Number of Residues	5
Details	binding site for residue MG A 302

Chain	Residue
A	G5P301
A	HOH411
A	HOH421
A	HOH452
A	HOH457

site_id	AC3
Number of Residues	38
Details	binding site for residue G5P B 301

Chain	Residue
B	PRO16
B	GLY17
B	SER18
B	GLY19
B	LYS20
B	GLY21
B	THR22
B	SER38
B	ILE60
B	LYS64
B	LEU65
B	ILE66
B	MET71
B	GLY91
B	PHE92
B	ARG94
B	GLN98
B	ARG124
B	ARG128
B	TYR138
B	ASN139
B	PHE142
B	ARG161
B	ARG172
B	GLU200
B	THR201
B	MG302
B	HOH417
B	HOH418
B	HOH429
B	HOH448
B	HOH450
B	HOH453
B	HOH456
B	HOH460
B	HOH468
B	HOH469
B	HOH470

site_id	AC4
Number of Residues	3
Details	binding site for residue MG B 302

Chain	Residue
B	G5P301
B	HOH443
B	HOH448

site_id	AC5
Number of Residues	35
Details	binding site for residue G5P C 301

Chain	Residue
C	LEU42
C	ILE60
C	LYS64
C	LEU65
C	ILE66
C	MET71
C	GLY91
C	PHE92
C	ARG94
C	GLN98
C	ARG124
C	ARG128
C	VAL137
C	TYR138
C	ASN139
C	PHE142
C	ARG161
C	ARG172
C	GLU200
C	THR201
C	MG302
C	HOH415
C	HOH417
C	HOH435
C	HOH438
C	HOH443
C	PRO16
C	GLY17
C	SER18
C	GLY19
C	LYS20
C	GLY21
C	THR22
C	SER38
C	GLY39

site_id	AC6
Number of Residues	2
Details	binding site for residue MG C 302

Chain	Residue
C	G5P301
C	HOH403

site_id	AC7
Number of Residues	40
Details	binding site for residue G5P D 301

Chain	Residue
D	PRO16
D	GLY17
D	SER18
D	GLY19
D	LYS20
D	GLY21
D	THR22
D	SER38
D	LEU42
D	ARG43
D	ILE60
D	LYS64
D	LEU65
D	ILE66
D	MET71
D	GLY91
D	PHE92
D	ARG94
D	GLN98
D	ARG124
D	ARG128
D	VAL137
D	TYR138
D	ASN139
D	PHE142
D	ARG161
D	ASP163
D	ARG172
D	GLU200
D	THR201
D	MG302
D	HOH404
D	HOH429
D	HOH433
D	HOH440
D	HOH441
D	HOH447
D	HOH486
D	HOH488
D	HOH489

site_id	AC8
Number of Residues	5
Details	binding site for residue MG D 302

Chain	Residue
D	G5P301
D	HOH409
D	HOH433
D	HOH451
D	HOH488

site_id	AC9
Number of Residues	43
Details	binding site for residue G5P E 301

Chain	Residue
E	PRO16
E	GLY17
E	SER18
E	GLY19
E	LYS20
E	GLY21
E	THR22
E	SER38
E	GLY39
E	ARG43
E	ILE60
E	LYS64
E	LEU65
E	ILE66
E	MET71
E	GLY91
E	ARG94
E	GLN98
E	ARG124
E	ARG128
E	VAL137
E	TYR138
E	ASN139
E	PHE142
E	ARG161
E	ARG172
E	GLU200
E	THR201
E	MG302
E	HOH409
E	HOH411
E	HOH424
E	HOH433
E	HOH437
E	HOH443
E	HOH448
E	HOH461
E	HOH467
E	HOH470
E	HOH479
E	HOH486
E	HOH502
E	HOH505

site_id	AD1
Number of Residues	5
Details	binding site for residue MG E 302

Chain	Residue
E	G5P301
E	HOH411
E	HOH416
E	HOH424
E	HOH502

site_id	AD2
Number of Residues	41
Details	binding site for residue G5P F 301

Chain	Residue
F	GLY17
F	SER18
F	GLY19
F	LYS20
F	GLY21
F	THR22
F	SER38
F	GLY39
F	ARG43
F	ILE60
F	LYS64
F	LEU65
F	ILE66
F	MET71
F	GLY91
F	PHE92
F	ARG94
F	GLN98
F	ARG124
F	ARG128
F	VAL137
F	TYR138
F	ASN139
F	PHE142
F	ARG161
F	ARG172
F	GLU200
F	THR201
F	MG302
F	HOH407
F	HOH413
F	HOH424
F	HOH427
F	HOH431
F	HOH433
F	HOH452
F	HOH456
F	HOH457
F	HOH460
F	HOH465
F	HOH507

site_id	AD3
Number of Residues	5
Details	binding site for residue MG F 302

Chain	Residue
F	G5P301
F	HOH404
F	HOH408
F	HOH413
F	HOH427

Functional Information from PROSITE/UniProt

site_id	PS00113
Number of Residues	12
Details	ADENYLATE_KINASE Adenylate kinase signature. WLLDGFPRtlpQ

Chain	Residue	Details
A	TRP87-GLN98

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	174
Details	Region: {"description":"NMP","evidences":[{"source":"HAMAP-Rule","id":"MF_03169","evidenceCode":"ECO:0000255"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"MAY-2005","submissionDatabase":"PDB data bank","title":"Structure of human adenylate kinase 3-like 1.","authoringGroup":["Structural genomics consortium (SGC)"]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	222
Details	Region: {"description":"LID","evidences":[{"source":"HAMAP-Rule","id":"MF_03169","evidenceCode":"ECO:0000255"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"MAY-2005","submissionDatabase":"PDB data bank","title":"Structure of human adenylate kinase 3-like 1.","authoringGroup":["Structural genomics consortium (SGC)"]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	96
Details	Binding site: {"evidences":[{"source":"PubMed","id":"32822537","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"6ZJB","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"P08760","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	12
Details	Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"Q9WTP7","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	12
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"Q9WTP7","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	6
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"Q9WTP7","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	24
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q9WTP7","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

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