Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5C3Y

Structure of human ribokinase crystallized with AMPPNP

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
E	0000166	molecular_function	nucleotide binding
E	0004747	molecular_function	ribokinase activity
E	0005515	molecular_function	protein binding
E	0005524	molecular_function	ATP binding
E	0005634	cellular_component	nucleus
E	0005737	cellular_component	cytoplasm
E	0005829	cellular_component	cytosol
E	0006014	biological_process	D-ribose metabolic process
E	0006098	biological_process	pentose-phosphate shunt
E	0016301	molecular_function	kinase activity
E	0016740	molecular_function	transferase activity
E	0019303	biological_process	D-ribose catabolic process
E	0042802	molecular_function	identical protein binding
E	0046835	biological_process	carbohydrate phosphorylation
E	0046872	molecular_function	metal ion binding
F	0000166	molecular_function	nucleotide binding
F	0004747	molecular_function	ribokinase activity
F	0005515	molecular_function	protein binding
F	0005524	molecular_function	ATP binding
F	0005634	cellular_component	nucleus
F	0005737	cellular_component	cytoplasm
F	0005829	cellular_component	cytosol
F	0006014	biological_process	D-ribose metabolic process
F	0006098	biological_process	pentose-phosphate shunt
F	0016301	molecular_function	kinase activity
F	0016740	molecular_function	transferase activity
F	0019303	biological_process	D-ribose catabolic process
F	0042802	molecular_function	identical protein binding
F	0046835	biological_process	carbohydrate phosphorylation
F	0046872	molecular_function	metal ion binding
G	0000166	molecular_function	nucleotide binding
G	0004747	molecular_function	ribokinase activity
G	0005515	molecular_function	protein binding
G	0005524	molecular_function	ATP binding
G	0005634	cellular_component	nucleus
G	0005737	cellular_component	cytoplasm
G	0005829	cellular_component	cytosol
G	0006014	biological_process	D-ribose metabolic process
G	0006098	biological_process	pentose-phosphate shunt
G	0016301	molecular_function	kinase activity
G	0016740	molecular_function	transferase activity
G	0019303	biological_process	D-ribose catabolic process
G	0042802	molecular_function	identical protein binding
G	0046835	biological_process	carbohydrate phosphorylation
G	0046872	molecular_function	metal ion binding
H	0000166	molecular_function	nucleotide binding
H	0004747	molecular_function	ribokinase activity
H	0005515	molecular_function	protein binding
H	0005524	molecular_function	ATP binding
H	0005634	cellular_component	nucleus
H	0005737	cellular_component	cytoplasm
H	0005829	cellular_component	cytosol
H	0006014	biological_process	D-ribose metabolic process
H	0006098	biological_process	pentose-phosphate shunt
H	0016301	molecular_function	kinase activity
H	0016740	molecular_function	transferase activity
H	0019303	biological_process	D-ribose catabolic process
H	0042802	molecular_function	identical protein binding
H	0046835	biological_process	carbohydrate phosphorylation
H	0046872	molecular_function	metal ion binding
I	0000166	molecular_function	nucleotide binding
I	0004747	molecular_function	ribokinase activity
I	0005515	molecular_function	protein binding
I	0005524	molecular_function	ATP binding
I	0005634	cellular_component	nucleus
I	0005737	cellular_component	cytoplasm
I	0005829	cellular_component	cytosol
I	0006014	biological_process	D-ribose metabolic process
I	0006098	biological_process	pentose-phosphate shunt
I	0016301	molecular_function	kinase activity
I	0016740	molecular_function	transferase activity
I	0019303	biological_process	D-ribose catabolic process
I	0042802	molecular_function	identical protein binding
I	0046835	biological_process	carbohydrate phosphorylation
I	0046872	molecular_function	metal ion binding
J	0000166	molecular_function	nucleotide binding
J	0004747	molecular_function	ribokinase activity
J	0005515	molecular_function	protein binding
J	0005524	molecular_function	ATP binding
J	0005634	cellular_component	nucleus
J	0005737	cellular_component	cytoplasm
J	0005829	cellular_component	cytosol
J	0006014	biological_process	D-ribose metabolic process
J	0006098	biological_process	pentose-phosphate shunt
J	0016301	molecular_function	kinase activity
J	0016740	molecular_function	transferase activity
J	0019303	biological_process	D-ribose catabolic process
J	0042802	molecular_function	identical protein binding
J	0046835	biological_process	carbohydrate phosphorylation
J	0046872	molecular_function	metal ion binding
K	0000166	molecular_function	nucleotide binding
K	0004747	molecular_function	ribokinase activity
K	0005515	molecular_function	protein binding
K	0005524	molecular_function	ATP binding
K	0005634	cellular_component	nucleus
K	0005737	cellular_component	cytoplasm
K	0005829	cellular_component	cytosol
K	0006014	biological_process	D-ribose metabolic process
K	0006098	biological_process	pentose-phosphate shunt
K	0016301	molecular_function	kinase activity
K	0016740	molecular_function	transferase activity
K	0019303	biological_process	D-ribose catabolic process
K	0042802	molecular_function	identical protein binding
K	0046835	biological_process	carbohydrate phosphorylation
K	0046872	molecular_function	metal ion binding
L	0000166	molecular_function	nucleotide binding
L	0004747	molecular_function	ribokinase activity
L	0005515	molecular_function	protein binding
L	0005524	molecular_function	ATP binding
L	0005634	cellular_component	nucleus
L	0005737	cellular_component	cytoplasm
L	0005829	cellular_component	cytosol
L	0006014	biological_process	D-ribose metabolic process
L	0006098	biological_process	pentose-phosphate shunt
L	0016301	molecular_function	kinase activity
L	0016740	molecular_function	transferase activity
L	0019303	biological_process	D-ribose catabolic process
L	0042802	molecular_function	identical protein binding
L	0046835	biological_process	carbohydrate phosphorylation
L	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	12
Details	binding site for residue AN2 A 401

Chain	Residue
A	THR235
A	ALA298
A	ALA299
A	HOH519
A	GLY237
A	GLY240
A	VAL259
A	THR264
A	GLY266
A	ALA267
A	GLY268
A	ASN295

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	HOH507
A	HOH526

site_id	AC3
Number of Residues	5
Details	binding site for residue NA A 403

Chain	Residue
A	HOH505
A	HOH512
A	HOH519
A	HOH535
A	HOH536

site_id	AC4
Number of Residues	13
Details	binding site for residue AN2 B 401

Chain	Residue
B	ASN199
B	THR235
B	GLY237
B	GLY240
B	VAL259
B	THR264
B	GLY266
B	ALA267
B	GLY268
B	ASN295
B	ALA298
B	HOH542
B	HOH549

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

Chain	Residue
B	ASP263
B	SER301
B	ALA304
B	SER310
B	HOH510
B	HOH529

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

Chain	Residue
B	HOH504
B	HOH511
B	HOH519
B	HOH542
B	HOH571
B	HOH574

site_id	AC7
Number of Residues	16
Details	binding site for residue AN2 C 401

Chain	Residue
C	ASN199
C	THR235
C	GLY237
C	ALA238
C	GLY240
C	VAL259
C	THR264
C	GLY266
C	ALA267
C	GLY268
C	ASN295
C	ALA298
C	ALA299
C	HOH550
C	HOH561
C	HOH568

site_id	AC8
Number of Residues	6
Details	binding site for residue NA C 402

Chain	Residue
C	ASP263
C	SER301
C	ALA304
C	SER310
C	HOH505
C	HOH512

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

Chain	Residue
C	HOH501
C	HOH502
C	HOH524
C	HOH540
C	HOH550
C	HOH561

site_id	AD1
Number of Residues	12
Details	binding site for residue AN2 D 401

Chain	Residue
D	THR235
D	GLY237
D	GLY240
D	VAL259
D	THR264
D	ALA267
D	GLY268
D	ASN295
D	ALA298
D	ALA299
D	HOH501
D	HOH515

site_id	AD2
Number of Residues	6
Details	binding site for residue NA D 402

Chain	Residue
D	ASP263
D	SER301
D	ALA304
D	SER310
D	HOH516
D	HOH517

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

Chain	Residue
D	HOH560
D	HOH511
D	HOH512
D	HOH527
D	HOH547
D	HOH558

site_id	AD4
Number of Residues	14
Details	binding site for residue AN2 E 401

Chain	Residue
E	ASN199
E	THR235
E	GLY237
E	GLY240
E	VAL259
E	THR264
E	ALA267
E	GLY268
E	ASN295
E	ALA298
E	ALA299
E	HOH516
E	HOH529
E	HOH553

site_id	AD5
Number of Residues	6
Details	binding site for residue NA E 402

Chain	Residue
E	ASP263
E	SER301
E	ALA304
E	SER310
E	HOH517
E	HOH519

site_id	AD6
Number of Residues	6
Details	binding site for residue NA E 403

Chain	Residue
E	HOH531
E	HOH534
E	HOH542
E	HOH553
E	HOH560
E	HOH577

site_id	AD7
Number of Residues	14
Details	binding site for residue AN2 F 401

Chain	Residue
F	THR235
F	GLY237
F	GLY240
F	VAL259
F	ALA261
F	THR264
F	GLY266
F	ALA267
F	GLY268
F	ASN295
F	ALA298
F	ALA299
F	VAL302
F	HOH523

site_id	AD8
Number of Residues	6
Details	binding site for residue NA F 402

Chain	Residue
F	ASP263
F	SER301
F	ALA304
F	SER310
F	HOH509
F	HOH522

site_id	AD9
Number of Residues	7
Details	binding site for residue NA F 403

Chain	Residue
F	ASN199
F	HOH501
F	HOH516
F	HOH523
F	HOH527
F	HOH534
F	HOH544

site_id	AE1
Number of Residues	16
Details	binding site for residue AN2 G 401

Chain	Residue
G	THR235
G	GLY237
G	ALA238
G	GLY240
G	VAL259
G	THR264
G	ALA267
G	GLY268
G	ASN295
G	ALA298
G	ALA299
G	HOH502
G	HOH506
G	HOH507
G	HOH521
G	HOH531

site_id	AE2
Number of Residues	6
Details	binding site for residue NA G 402

Chain	Residue
G	ASP263
G	SER301
G	ALA304
G	SER310
G	HOH517
G	HOH535

site_id	AE3
Number of Residues	6
Details	binding site for residue NA G 403

Chain	Residue
G	HOH506
G	HOH523
G	HOH525
G	HOH526
G	HOH555
G	HOH578

site_id	AE4
Number of Residues	13
Details	binding site for residue AN2 H 401

Chain	Residue
H	THR235
H	GLY237
H	ALA238
H	GLY240
H	VAL259
H	THR264
H	GLY268
H	ASN295
H	ALA298
H	HOH501
H	HOH522
H	HOH523
H	HOH545

site_id	AE5
Number of Residues	6
Details	binding site for residue NA H 402

Chain	Residue
H	ASP263
H	SER301
H	ALA304
H	SER310
H	HOH509
H	HOH514

site_id	AE6
Number of Residues	6
Details	binding site for residue NA H 403

Chain	Residue
H	HOH522
H	HOH524
H	HOH526
H	HOH539
H	HOH545
H	HOH568

site_id	AE7
Number of Residues	14
Details	binding site for residue AN2 I 401

Chain	Residue
I	ASN199
I	THR235
I	GLY237
I	ALA238
I	GLY240
I	VAL259
I	THR264
I	GLY266
I	ALA267
I	GLY268
I	ASN295
I	ALA298
I	ALA299
I	HOH538

site_id	AE8
Number of Residues	6
Details	binding site for residue NA I 402

Chain	Residue
I	ASP263
I	SER301
I	ALA304
I	SER310
I	HOH519
I	HOH522

site_id	AE9
Number of Residues	5
Details	binding site for residue NA I 403

Chain	Residue
I	HOH513
I	HOH517
I	HOH520
I	HOH532
I	HOH538

site_id	AF1
Number of Residues	13
Details	binding site for residue AN2 J 401

Chain	Residue
J	THR235
J	GLY237
J	ALA238
J	GLY240
J	VAL259
J	THR264
J	ALA267
J	GLY268
J	ASN295
J	ALA298
J	ALA299
J	HOH514
J	HOH521

site_id	AF2
Number of Residues	6
Details	binding site for residue NA J 402

Chain	Residue
J	ASP263
J	SER301
J	ALA304
J	SER310
J	HOH505
J	HOH513

site_id	AF3
Number of Residues	6
Details	binding site for residue NA J 403

Chain	Residue
J	HOH503
J	HOH504
J	HOH514
J	HOH521
J	HOH528
J	HOH530

site_id	AF4
Number of Residues	14
Details	binding site for residue AN2 K 401

Chain	Residue
K	ASN199
K	THR235
K	GLY237
K	ALA238
K	GLY240
K	VAL259
K	THR264
K	GLY266
K	ALA267
K	GLY268
K	ASN295
K	ALA298
K	ALA299
K	HOH541

site_id	AF5
Number of Residues	6
Details	binding site for residue NA K 402

Chain	Residue
K	ASP263
K	SER301
K	ALA304
K	SER310
K	HOH507
K	HOH536

site_id	AF6
Number of Residues	6
Details	binding site for residue NA K 403

Chain	Residue
K	HOH501
K	HOH508
K	HOH526
K	HOH541
K	HOH544
K	HOH546

site_id	AF7
Number of Residues	15
Details	binding site for residue AN2 L 401

Chain	Residue
L	ASN199
L	THR235
L	GLY237
L	GLY240
L	VAL259
L	THR264
L	ALA267
L	GLY268
L	ASN295
L	ALA298
L	ALA299
L	HOH501
L	HOH504
L	HOH517
L	HOH530

site_id	AF8
Number of Residues	6
Details	binding site for residue NA L 402

Chain	Residue
L	ASP263
L	SER301
L	ALA304
L	SER310
L	HOH516
L	HOH522

site_id	AF9
Number of Residues	6
Details	binding site for residue NA L 403

Chain	Residue
L	HOH515
L	HOH521
L	HOH524
L	HOH530
L	HOH534
L	HOH539

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	12
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	120
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	108
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	48
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)