Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5C41

Crystal structure of human ribokinase in complex with AMPPCP in P21 spacegroup and with 4 protomers

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0004747	molecular_function	ribokinase activity
A	0005515	molecular_function	protein binding
A	0005524	molecular_function	ATP binding
A	0005634	cellular_component	nucleus
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0006014	biological_process	D-ribose metabolic process
A	0006098	biological_process	pentose-phosphate shunt
A	0016301	molecular_function	kinase activity
A	0016740	molecular_function	transferase activity
A	0019303	biological_process	D-ribose catabolic process
A	0042802	molecular_function	identical protein binding
A	0046835	biological_process	carbohydrate phosphorylation
A	0046872	molecular_function	metal ion binding
B	0000166	molecular_function	nucleotide binding
B	0004747	molecular_function	ribokinase activity
B	0005515	molecular_function	protein binding
B	0005524	molecular_function	ATP binding
B	0005634	cellular_component	nucleus
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0006014	biological_process	D-ribose metabolic process
B	0006098	biological_process	pentose-phosphate shunt
B	0016301	molecular_function	kinase activity
B	0016740	molecular_function	transferase activity
B	0019303	biological_process	D-ribose catabolic process
B	0042802	molecular_function	identical protein binding
B	0046835	biological_process	carbohydrate phosphorylation
B	0046872	molecular_function	metal ion binding
C	0000166	molecular_function	nucleotide binding
C	0004747	molecular_function	ribokinase activity
C	0005515	molecular_function	protein binding
C	0005524	molecular_function	ATP binding
C	0005634	cellular_component	nucleus
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0006014	biological_process	D-ribose metabolic process
C	0006098	biological_process	pentose-phosphate shunt
C	0016301	molecular_function	kinase activity
C	0016740	molecular_function	transferase activity
C	0019303	biological_process	D-ribose catabolic process
C	0042802	molecular_function	identical protein binding
C	0046835	biological_process	carbohydrate phosphorylation
C	0046872	molecular_function	metal ion binding
D	0000166	molecular_function	nucleotide binding
D	0004747	molecular_function	ribokinase activity
D	0005515	molecular_function	protein binding
D	0005524	molecular_function	ATP binding
D	0005634	cellular_component	nucleus
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0006014	biological_process	D-ribose metabolic process
D	0006098	biological_process	pentose-phosphate shunt
D	0016301	molecular_function	kinase activity
D	0016740	molecular_function	transferase activity
D	0019303	biological_process	D-ribose catabolic process
D	0042802	molecular_function	identical protein binding
D	0046835	biological_process	carbohydrate phosphorylation
D	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	27
Details	binding site for residue ACP A 401

Chain	Residue
A	ASN199
A	GLY268
A	ASN295
A	ALA298
A	ALA299
A	NA403
A	HOH501
A	HOH507
A	HOH515
A	HOH525
A	HOH530
A	THR235
A	HOH560
A	HOH576
A	HOH596
A	HOH615
A	HOH621
A	HOH684
A	HOH686
A	HOH688
A	LEU236
A	GLY237
A	ALA238
A	GLY240
A	VAL259
A	THR264
A	ALA267

site_id	AC2
Number of Residues	6
Details	binding site for residue NA A 402

Chain	Residue
A	ASP263
A	SER301
A	ALA304
A	SER310
A	HOH579
A	HOH629

site_id	AC3
Number of Residues	7
Details	binding site for residue NA A 403

Chain	Residue
A	ACP401
A	HOH501
A	HOH513
A	HOH530
A	HOH569
A	HOH615
A	HOH655

site_id	AC4
Number of Residues	28
Details	binding site for residue ACP B 401

Chain	Residue
B	ASN199
B	THR235
B	GLY237
B	ALA238
B	GLY240
B	THR256
B	GLU257
B	VAL259
B	THR264
B	THR265
B	GLY266
B	ALA267
B	GLY268
B	ASN295
B	ALA298
B	ALA299
B	HOH510
B	HOH542
B	HOH543
B	HOH548
B	HOH572
B	HOH573
B	HOH577
B	HOH637
B	HOH644
B	HOH659
B	HOH663
B	HOH671

site_id	AC5
Number of Residues	6
Details	binding site for residue NA B 402

Chain	Residue
B	ASP263
B	SER301
B	ALA304
B	GLY306
B	SER310
B	HOH624

site_id	AC6
Number of Residues	6
Details	binding site for residue NA B 403

Chain	Residue
B	HOH523
B	HOH536
B	HOH542
B	HOH612
B	HOH641
B	HOH663

site_id	AC7
Number of Residues	25
Details	binding site for residue ACP C 401

Chain	Residue
C	HOH556
C	HOH578
C	HOH583
C	HOH593
C	HOH610
C	HOH628
C	ASN199
C	THR235
C	LEU236
C	GLY237
C	ALA238
C	GLY240
C	VAL259
C	ALA267
C	GLY268
C	ASN295
C	ALA298
C	ALA299
C	NA403
C	HOH504
C	HOH508
C	HOH520
C	HOH537
C	HOH538
C	HOH550

site_id	AC8
Number of Residues	7
Details	binding site for residue NA C 402

Chain	Residue
C	ASP263
C	SER301
C	ALA304
C	GLY306
C	SER310
C	HOH502
C	HOH629

site_id	AC9
Number of Residues	6
Details	binding site for residue NA C 403

Chain	Residue
C	ACP401
C	HOH519
C	HOH520
C	HOH574
C	HOH685
C	HOH710

site_id	AD1
Number of Residues	17
Details	binding site for residue ACP D 401

Chain	Residue
D	ASN199
D	THR235
D	GLY237
D	ALA238
D	GLY240
D	VAL259
D	THR264
D	ALA267
D	GLY268
D	ASN295
D	ALA298
D	ALA299
D	HOH510
D	HOH516
D	HOH524
D	HOH577
D	HOH585

site_id	AD2
Number of Residues	5
Details	binding site for residue PO4 D 402

Chain	Residue
D	TYR282
D	PRO283
D	ASN284
D	LEU285
D	HOH547

site_id	AD3
Number of Residues	6
Details	binding site for residue NA D 403

Chain	Residue
D	ASP263
D	SER301
D	ALA304
D	SER310
D	HOH581
D	HOH594

site_id	AD4
Number of Residues	6
Details	binding site for residue NA D 404

Chain	Residue
D	HOH511
D	HOH521
D	HOH524
D	HOH552
D	HOH577
D	HOH611

Functional Information from PROSITE/UniProt

site_id	PS00584
Number of Residues	14
Details	PFKB_KINASES_2 pfkB family of carbohydrate kinases signature 2. DTtGAGDsfvGALA

Chain	Residue	Details
A	ASP263-ALA276

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	Active site: {"description":"Proton acceptor","evidences":[{"source":"UniProtKB","id":"P0A9J6","evidenceCode":"ECO:0000250"},{"source":"HAMAP-Rule","id":"MF_03215","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	40
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"P0A9J6","evidenceCode":"ECO:0000250"},{"source":"HAMAP-Rule","id":"MF_03215","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	36
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_03215","evidenceCode":"ECO:0000255"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"JAN-2006","submissionDatabase":"PDB data bank","title":"Crystal structure of human ribokinase.","authoringGroup":["Structural genomics consortium (SGC)"]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	16
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_03215","evidenceCode":"ECO:0000255"},{"source":"Reference","evidenceCode":"ECO:0000305","citation":{"citationType":"submission","publicationDate":"JAN-2006","submissionDatabase":"PDB data bank","title":"Crystal structure of human ribokinase.","authoringGroup":["Structural genomics consortium (SGC)"]}}]}

Chain

Residue

Details

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