6ZJB

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

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0004017	molecular_function	AMP kinase activity
A	0005515	molecular_function	protein binding
A	0005524	molecular_function	ATP binding
A	0005525	molecular_function	GTP binding
A	0005737	cellular_component	cytoplasm
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	0016301	molecular_function	kinase activity
A	0016740	molecular_function	transferase activity
A	0016776	molecular_function	phosphotransferase activity, phosphate group as acceptor
A	0016874	molecular_function	ligase activity
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	0000166	molecular_function	nucleotide binding
B	0004017	molecular_function	AMP kinase activity
B	0005515	molecular_function	protein binding
B	0005524	molecular_function	ATP binding
B	0005525	molecular_function	GTP binding
B	0005737	cellular_component	cytoplasm
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	0016301	molecular_function	kinase activity
B	0016740	molecular_function	transferase activity
B	0016776	molecular_function	phosphotransferase activity, phosphate group as acceptor
B	0016874	molecular_function	ligase activity
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	0000166	molecular_function	nucleotide binding
C	0004017	molecular_function	AMP kinase activity
C	0005515	molecular_function	protein binding
C	0005524	molecular_function	ATP binding
C	0005525	molecular_function	GTP binding
C	0005737	cellular_component	cytoplasm
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	0016301	molecular_function	kinase activity
C	0016740	molecular_function	transferase activity
C	0016776	molecular_function	phosphotransferase activity, phosphate group as acceptor
C	0016874	molecular_function	ligase activity
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	0000166	molecular_function	nucleotide binding
D	0004017	molecular_function	AMP kinase activity
D	0005515	molecular_function	protein binding
D	0005524	molecular_function	ATP binding
D	0005525	molecular_function	GTP binding
D	0005737	cellular_component	cytoplasm
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	0016301	molecular_function	kinase activity
D	0016740	molecular_function	transferase activity
D	0016776	molecular_function	phosphotransferase activity, phosphate group as acceptor
D	0016874	molecular_function	ligase activity
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	0000166	molecular_function	nucleotide binding
E	0004017	molecular_function	AMP kinase activity
E	0005515	molecular_function	protein binding
E	0005524	molecular_function	ATP binding
E	0005525	molecular_function	GTP binding
E	0005737	cellular_component	cytoplasm
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	0016301	molecular_function	kinase activity
E	0016740	molecular_function	transferase activity
E	0016776	molecular_function	phosphotransferase activity, phosphate group as acceptor
E	0016874	molecular_function	ligase activity
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	0000166	molecular_function	nucleotide binding
F	0004017	molecular_function	AMP kinase activity
F	0005515	molecular_function	protein binding
F	0005524	molecular_function	ATP binding
F	0005525	molecular_function	GTP binding
F	0005737	cellular_component	cytoplasm
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	0016301	molecular_function	kinase activity
F	0016740	molecular_function	transferase activity
F	0016776	molecular_function	phosphotransferase activity, phosphate group as acceptor
F	0016874	molecular_function	ligase activity
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

---