Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1Z83

Crystal structure of human AK1A in complex with AP5A

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0001520	cellular_component	outer dense fiber
A	0004017	molecular_function	AMP kinase activity
A	0004550	molecular_function	nucleoside diphosphate kinase activity
A	0005524	molecular_function	ATP binding
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0006139	biological_process	nucleobase-containing compound metabolic process
A	0006172	biological_process	ADP biosynthetic process
A	0009142	biological_process	nucleoside triphosphate biosynthetic process
A	0015949	biological_process	nucleobase-containing small molecule interconversion
A	0016301	molecular_function	kinase activity
A	0016740	molecular_function	transferase activity
A	0019205	molecular_function	nucleobase-containing compound kinase activity
A	0036126	cellular_component	sperm flagellum
A	0046033	biological_process	AMP metabolic process
A	0046034	biological_process	ATP metabolic process
A	0046940	biological_process	nucleoside monophosphate phosphorylation
A	0047506	molecular_function	dAMP kinase activity
A	0050145	molecular_function	nucleoside monophosphate kinase activity
A	0070062	cellular_component	extracellular exosome
B	0000166	molecular_function	nucleotide binding
B	0001520	cellular_component	outer dense fiber
B	0004017	molecular_function	AMP kinase activity
B	0004550	molecular_function	nucleoside diphosphate kinase activity
B	0005524	molecular_function	ATP binding
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0006139	biological_process	nucleobase-containing compound metabolic process
B	0006172	biological_process	ADP biosynthetic process
B	0009142	biological_process	nucleoside triphosphate biosynthetic process
B	0015949	biological_process	nucleobase-containing small molecule interconversion
B	0016301	molecular_function	kinase activity
B	0016740	molecular_function	transferase activity
B	0019205	molecular_function	nucleobase-containing compound kinase activity
B	0036126	cellular_component	sperm flagellum
B	0046033	biological_process	AMP metabolic process
B	0046034	biological_process	ATP metabolic process
B	0046940	biological_process	nucleoside monophosphate phosphorylation
B	0047506	molecular_function	dAMP kinase activity
B	0050145	molecular_function	nucleoside monophosphate kinase activity
B	0070062	cellular_component	extracellular exosome
C	0000166	molecular_function	nucleotide binding
C	0001520	cellular_component	outer dense fiber
C	0004017	molecular_function	AMP kinase activity
C	0004550	molecular_function	nucleoside diphosphate kinase activity
C	0005524	molecular_function	ATP binding
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0006139	biological_process	nucleobase-containing compound metabolic process
C	0006172	biological_process	ADP biosynthetic process
C	0009142	biological_process	nucleoside triphosphate biosynthetic process
C	0015949	biological_process	nucleobase-containing small molecule interconversion
C	0016301	molecular_function	kinase activity
C	0016740	molecular_function	transferase activity
C	0019205	molecular_function	nucleobase-containing compound kinase activity
C	0036126	cellular_component	sperm flagellum
C	0046033	biological_process	AMP metabolic process
C	0046034	biological_process	ATP metabolic process
C	0046940	biological_process	nucleoside monophosphate phosphorylation
C	0047506	molecular_function	dAMP kinase activity
C	0050145	molecular_function	nucleoside monophosphate kinase activity
C	0070062	cellular_component	extracellular exosome

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN A 601

Chain	Residue
A	AP5631
A	HOH703
A	HOH704
A	HOH838
A	HOH845

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN B 611

Chain	Residue
B	HOH811
B	AP5632
B	HOH704
B	HOH776
B	HOH805

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN C 621

Chain	Residue
C	AP5633
C	HOH646
C	HOH647
C	HOH732
C	HOH741

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN A 641

Chain	Residue
A	GLU26
A	HIS36
A	GLU144
A	HOH840
A	HOH846

site_id	AC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN B 642

Chain	Residue
A	GLU70
A	ASP74
B	GLU70
B	GLU104
B	ARG108

site_id	AC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN B 643

Chain	Residue
B	GLU26
B	HIS36
B	HOH806
B	HOH812
C	GLU144

site_id	AC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN C 644

Chain	Residue
B	GLU144
C	GLU26
C	HIS36
C	HOH733
C	HOH742

site_id	AC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN C 645

Chain	Residue
C	GLU70
C	GLU70
C	ASP74
C	ASP74
C	ARG108

site_id	AC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 B 701

Chain	Residue
B	THR35
B	LYS83
B	THR86
B	SER87

site_id	BC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 A 702

Chain	Residue
A	ARG107
A	HOH858
B	ARG53

site_id	BC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 B 703

Chain	Residue
A	ALA82
A	LYS83
A	HOH872
B	SER0
B	MET1
B	HOH740

site_id	BC3
Number of Residues	43
Details	BINDING SITE FOR RESIDUE AP5 A 631

Chain	Residue
A	PRO17
A	GLY18
A	SER19
A	GLY20
A	LYS21
A	GLY22
A	THR23
A	THR39
A	GLY40
A	LEU43
A	ARG44
A	MET61
A	GLN65
A	LEU66
A	VAL67
A	GLY94
A	TYR95
A	ARG97
A	GLN101
A	ARG128
A	ARG132
A	ARG138
A	ARG149
A	GLY177
A	SER178
A	VAL179
A	ZN601
A	HOH703
A	HOH704
A	HOH707
A	HOH709
A	HOH710
A	HOH720
A	HOH723
A	HOH725
A	HOH732
A	HOH738
A	HOH755
A	HOH783
A	HOH789
A	HOH820
A	HOH838
A	HOH845

site_id	BC4
Number of Residues	40
Details	BINDING SITE FOR RESIDUE AP5 B 632

Chain	Residue
B	SER19
B	GLY20
B	LYS21
B	GLY22
B	THR23
B	THR39
B	GLY40
B	LEU43
B	ARG44
B	MET61
B	GLN65
B	LEU66
B	VAL67
B	GLY94
B	TYR95
B	ARG97
B	GLN101
B	ARG128
B	LEU129
B	ARG132
B	ARG138
B	ARG149
B	GLY177
B	VAL179
B	ZN611
B	HOH704
B	HOH705
B	HOH711
B	HOH726
B	HOH728
B	HOH776
B	HOH778
B	HOH797
B	HOH803
B	HOH805
B	HOH811
B	HOH838
B	GLY16
B	PRO17
B	GLY18

site_id	BC5
Number of Residues	41
Details	BINDING SITE FOR RESIDUE AP5 C 633

Chain	Residue
B	LYS63
C	GLY16
C	PRO17
C	GLY18
C	SER19
C	GLY20
C	LYS21
C	GLY22
C	THR23
C	THR39
C	GLY40
C	LEU43
C	ARG44
C	MET61
C	GLN65
C	LEU66
C	VAL67
C	GLY94
C	TYR95
C	ARG97
C	GLN101
C	ARG128
C	ARG132
C	ARG138
C	ARG149
C	GLY177
C	VAL179
C	ZN621
C	HOH646
C	HOH647
C	HOH649
C	HOH659
C	HOH663
C	HOH672
C	HOH674
C	HOH684
C	HOH688
C	HOH701
C	HOH703
C	HOH710
C	HOH732

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	PHE90-GLN101

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	87
Details	Region: {"description":"NMP","evidences":[{"source":"HAMAP-Rule","id":"MF_03171","evidenceCode":"ECO:0000255"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"MAR-2007","submissionDatabase":"PDB data bank","title":"Crystal structure of human AK1A in complex with AP5A.","authoringGroup":["Structural genomics consortium (SGC)"]}},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"DEC-2005","submissionDatabase":"PDB data bank","title":"Structure of adenylate kinase 1 in complex with P1, P4-di(adenosine)tetraphosphate.","authoringGroup":["Structural genomics consortium (SGC)"]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	30
Details	Region: {"description":"LID","evidences":[{"source":"HAMAP-Rule","id":"MF_03171","evidenceCode":"ECO:0000255"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"MAR-2007","submissionDatabase":"PDB data bank","title":"Crystal structure of human AK1A in complex with AP5A.","authoringGroup":["Structural genomics consortium (SGC)"]}},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"DEC-2005","submissionDatabase":"PDB data bank","title":"Structure of adenylate kinase 1 in complex with P1, P4-di(adenosine)tetraphosphate.","authoringGroup":["Structural genomics consortium (SGC)"]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	51
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_03171","evidenceCode":"ECO:0000255"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"MAR-2007","submissionDatabase":"PDB data bank","title":"Crystal structure of human AK1A in complex with AP5A.","authoringGroup":["Structural genomics consortium (SGC)"]}},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"DEC-2005","submissionDatabase":"PDB data bank","title":"Structure of adenylate kinase 1 in complex with P1, P4-di(adenosine)tetraphosphate.","authoringGroup":["Structural genomics consortium (SGC)"]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	3
Details	Modified residue: {"description":"N-acetylmethionine","evidences":[{"source":"HAMAP-Rule","id":"MF_03171","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"183954","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	3
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"24275569","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	CSA1
Number of Residues	6
Details	Annotated By Reference To The Literature 1zio

Chain	Residue	Details
A	ARG138
A	LYS21
A	ASP140
A	ARG149
A	ASP141
A	ARG132

site_id	CSA2
Number of Residues	6
Details	Annotated By Reference To The Literature 1zio

Chain	Residue	Details
B	ARG138
B	LYS21
B	ASP140
B	ARG149
B	ASP141
B	ARG132

site_id	CSA3
Number of Residues	6
Details	Annotated By Reference To The Literature 1zio

Chain	Residue	Details
C	ARG138
C	LYS21
C	ASP140
C	ARG149
C	ASP141
C	ARG132

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