2FV7 - JenaLib

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Title :   CRYSTAL STRUCTURE OF HUMAN RIBOKINASE

Authors :   W. M. Rabeh, W. Tempel, L. Nedyalkova, C. Arrowsmith, A. Edwards, M. Sun J. Weigelt, A. Bochkarev, H. Park, Structural Genomics Consortium

Date :   30 Jan 06 (Deposition) - 28 Feb 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A (1x),B (1x)

Keywords :   Ribokinase, Structural Genomics, Structural Genomics Consortium, Sgc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. M. Rabeh, W. Tempel, L. Nedyalkova, C. Arrowsmith, A. Edwards, M. Sundstrom, J. Weigelt, A. Bochkarev, H. Park, Structural Genomics Consortium (Sgc)
Crystal Structure Of Human Ribokinase
To Be Published
PubMed: search

Molecule 1 - RIBOKINASE
	Chains	:	A, B
	EC Number	:	2.7.1.15
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	P28A-LIC
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	RBKS, RBSK
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:	A (1x)	B (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 18)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	NA	2	Ligand/Ion	SODIUM ION
4	UNX	12	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 1 (2, 14)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	NA	-1	Ligand/Ion	SODIUM ION
4	UNX	12	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 2 (2, 7)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	NA	-1	Ligand/Ion	SODIUM ION
4	UNX	6	Ligand/Ion	UNKNOWN ATOM OR ION

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:263 , SER A:301 , ALA A:304 , SER A:310 , HOH A:878 , HOH A:879	BINDING SITE FOR RESIDUE NA A 403
02	AC2	SOFTWARE	ADP A:401 , HOH A:817 , HOH A:819 , HOH A:825	BINDING SITE FOR RESIDUE MG A 404
03	AC3	SOFTWARE	ASP B:263 , SER B:301 , ALA B:304 , SER B:310 , HOH B:845 , HOH B:853	BINDING SITE FOR RESIDUE NA B 405
04	AC4	SOFTWARE	ADP B:402 , HOH B:842 , HOH B:859 , HOH B:864 , HOH B:871	BINDING SITE FOR RESIDUE MG B 406
05	AC5	SOFTWARE	ASN A:199 , THR A:235 , LEU A:236 , GLY A:237 , GLY A:240 , THR A:256 , GLU A:257 , VAL A:259 , ALA A:267 , GLY A:268 , ASN A:295 , ALA A:298 , VAL A:302 , MG A:404 , HOH A:805 , HOH A:856	BINDING SITE FOR RESIDUE ADP A 401
06	AC6	SOFTWARE	ASN B:199 , THR B:235 , LEU B:236 , GLY B:237 , ALA B:238 , GLY B:240 , THR B:256 , GLU B:257 , VAL B:259 , GLY B:268 , ASN B:295 , ALA B:298 , MG B:406 , HOH B:871	BINDING SITE FOR RESIDUE ADP B 402
07	AC7	SOFTWARE	VAL A:21 , GLY A:22 , CYS A:151 , GLN A:152 , ILE A:155 , SER A:160 , HOH A:801	BINDING SITE FOR RESIDUE UNX A 501
08	AC8	SOFTWARE	VAL B:21 , GLN B:152 , ILE B:155 , SER B:160 , HOH B:807	BINDING SITE FOR RESIDUE UNX B 502
09	AC9	SOFTWARE	GLY B:53 , ASN B:57	BINDING SITE FOR RESIDUE UNX B 503
10	BC1	SOFTWARE	LYS B:173	BINDING SITE FOR RESIDUE UNX B 504
11	BC2	SOFTWARE	ASP B:78	BINDING SITE FOR RESIDUE UNX B 505
12	BC3	SOFTWARE	LYS A:173 , ASP A:194	BINDING SITE FOR RESIDUE UNX A 506
13	BC4	SOFTWARE	GLY A:171 , LYS B:46	BINDING SITE FOR RESIDUE UNX A 507
14	BC5	SOFTWARE	LYS A:54 , ASP A:269 , HOH A:856	BINDING SITE FOR RESIDUE UNX A 510
15	BC6	SOFTWARE	PHE B:51	BINDING SITE FOR RESIDUE UNX B 511

(no "SS Bond" information available for 2FV7)

Asymmetric Unit

No.	Residues
1	Ala A:179	-	Pro A:180
2	Ala B:179	-	Pro B:180

(no "SAP(SNP)/Variant" information available for 2FV7)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PFKB_KINASES_2	PS00584	pfkB family of carbohydrate kinases signature 2.	RBSK_HUMAN	263-276	2	A:263-276 B:263-276

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PFKB_KINASES_2	PS00584	pfkB family of carbohydrate kinases signature 2.	RBSK_HUMAN	263-276	2	A:263-276 B:263-276

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PFKB_KINASES_2	PS00584	pfkB family of carbohydrate kinases signature 2.	RBSK_HUMAN	263-276	2	A:263-276 B:263-276

Asymmetric Unit (8, 16)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000302188	1a	ENSE00001260860	chr2:28113965-28113124	842	RBSK_HUMAN	1-30	30	2	A:15-30 B:15-30	16 16
1.4b	ENST00000302188	4b	ENSE00001709591	chr2:28081438-28081306	133	RBSK_HUMAN	30-74	45	2	A:30-74 B:30-74	45 45
1.5	ENST00000302188	5	ENSE00001794033	chr2:28070964-28070901	64	RBSK_HUMAN	75-96	22	2	A:75-96 B:75-96	22 22
1.6	ENST00000302188	6	ENSE00001785669	chr2:28069971-28069909	63	RBSK_HUMAN	96-117	22	2	A:96-117 B:96-117	22 22
1.7a	ENST00000302188	7a	ENSE00001600483	chr2:28066098-28065934	165	RBSK_HUMAN	117-172	56	2	A:117-172 B:117-172	56 56
1.8	ENST00000302188	8	ENSE00001652758	chr2:28055644-28055553	92	RBSK_HUMAN	172-202	31	2	A:172-202 B:172-202	31 31
1.9	ENST00000302188	9	ENSE00001766843	chr2:28050622-28050434	189	RBSK_HUMAN	203-265	63	2	A:203-265 B:203-265	63 63
1.11b	ENST00000302188	11b	ENSE00001260853	chr2:28004655-28004231	425	RBSK_HUMAN	266-322	57	2	A:266-322 B:266-322	57 57

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:308
 aligned with RBSK_HUMAN | Q9H477 from UniProtKB/Swiss-Prot  Length:322

    Alignment length:308
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314        
           RBSK_HUMAN    15 VAAVVVVGSCMTDLVSLTSRLPKTGETIHGHKFFIGFGGKGANQCVQAARLGAMTSMVCKVGKDSFGNDYIENLKQNDISTEFTYQTKDAATGTASIIVNNEGQNIIVIVAGANLLLNTEDLRAAANVISRAKVMVCQLEITPATSLEALTMARRSGVKTLFNPAPAIADLDPQFYTLSDVFCCNESEAEILTGLTVGSAADAGEAALVLLKRGCQVVIITLGAEGCVVLSQTEPEPKHIPTEKVKAVDTTGAGDSFVGALAFYLAYYPNLSLEDMLNRSNFIAAVSVQAAGTQSSYPYKKDLPLTLF 322
               SCOP domains d2fv7a1 A:15-322 Ribokinase                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 2fv7A00 A:15-322  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...eeeeeee..............eeeeeeehhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhh..ee...eeee.....eeeeeee.....eeeeeehhhhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhhh..eeee..........hhhhhh..eeeeehhhhhhhhh....hhhhhhhhhhhhhh....eeeee.hhh.eeeee......eee...........hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFKB_KINASES_2---------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a       --------------------------------------------Exon 1.5  PDB: A:75-96--------------------Exon 1.7a  PDB: A:117-172 UniProt: 117-172              ------------------------------Exon 1.9  PDB: A:203-265 UniProt: 203-265                      Exon 1.11b  PDB: A:266-322 UniProt: 266-322               Transcript 1 (1)
           Transcript 1 (2) ---------------Exon 1.4b  PDB: A:30-74 UniProt: 30-74       ---------------------Exon 1.6  PDB: A:96-11------------------------------------------------------Exon 1.8  PDB: A:172-202       ------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 2fv7 A  15 VAAVVVVGSCMTDLVSLTSRLPKTGETIHGHKFFIGFGGKGANQCVQAARLGAMTSMVCKVGKDSFGNDYIENLKQNDISTEFTYQTKDAATGTASIIVNNEGQNIIVIVAGANLLLNTEDLRAAANVISRAKVMVCQLEITPATSLEALTMARRSGVKTLFNPAPAIADLDPQFYTLSDVFCCNESEAEILTGLTVGSAADAGEAALVLLKRGCQVVIITLGAEGCVVLSQTEPEPKHIPTEKVKAVDTTGAGDSFVGALAFYLAYYPNLSLEDMLNRSNFIAAVSVQAAGTQSSYPYKKDLPLTLF 322
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314

Chain B from PDB  Type:PROTEIN  Length:308
 aligned with RBSK_HUMAN | Q9H477 from UniProtKB/Swiss-Prot  Length:322

    Alignment length:308
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314        
           RBSK_HUMAN    15 VAAVVVVGSCMTDLVSLTSRLPKTGETIHGHKFFIGFGGKGANQCVQAARLGAMTSMVCKVGKDSFGNDYIENLKQNDISTEFTYQTKDAATGTASIIVNNEGQNIIVIVAGANLLLNTEDLRAAANVISRAKVMVCQLEITPATSLEALTMARRSGVKTLFNPAPAIADLDPQFYTLSDVFCCNESEAEILTGLTVGSAADAGEAALVLLKRGCQVVIITLGAEGCVVLSQTEPEPKHIPTEKVKAVDTTGAGDSFVGALAFYLAYYPNLSLEDMLNRSNFIAAVSVQAAGTQSSYPYKKDLPLTLF 322
               SCOP domains d2fv7b_ B: Ribokinase                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2fv7B00 B:15-322  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...eeeeeee..............eeeeeeehhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhhh......eeee.....eeeeeee.....eeeeeehhhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhh..eeee..........hhhhhh..eeeeehhhhhhhhh....hhhhhhhhhhhhhhh...eeeee.hhh.eeeee......eee...........hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFKB_KINASES_2---------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a       --------------------------------------------Exon 1.5  PDB: B:75-96--------------------Exon 1.7a  PDB: B:117-172 UniProt: 117-172              ------------------------------Exon 1.9  PDB: B:203-265 UniProt: 203-265                      Exon 1.11b  PDB: B:266-322 UniProt: 266-322               Transcript 1 (1)
           Transcript 1 (2) ---------------Exon 1.4b  PDB: B:30-74 UniProt: 30-74       ---------------------Exon 1.6  PDB: B:96-11------------------------------------------------------Exon 1.8  PDB: B:172-202       ------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 2fv7 B  15 VAAVVVVGSCMTDLVSLTSRLPKTGETIHGHKFFIGFGGKGANQCVQAARLGAMTSMVCKVGKDSFGNDYIENLKQNDISTEFTYQTKDAATGTASIIVNNEGQNIIVIVAGANLLLNTEDLRAAANVISRAKVMVCQLEITPATSLEALTMARRSGVKTLFNPAPAIADLDPQFYTLSDVFCCNESEAEILTGLTVGSAADAGEAALVLLKRGCQVVIITLGAEGCVVLSQTEPEPKHIPTEKVKAVDTTGAGDSFVGALAFYLAYYPNLSLEDMLNRSNFIAAVSVQAAGTQSSYPYKKDLPLTLF 322
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314

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	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a/b) (23833)

Fold: Ribokinase-like (226)

Superfamily: Ribokinase-like (189)

Family: Ribokinase-like (36)

Protein domain: Ribokinase (7)

Human (Homo sapiens) [TaxId: 9606] (1)

1a	d2fv7a1	A:15-322
1b	d2fv7b_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase (109)

Homologous Superfamily: [code=3.40.1190.20, no name defined] (73)

Human (Homo sapiens) (10)

1a	2fv7A00	A:15-322
1b	2fv7B00	B:15-322

(no "Pfam Domain" information available for 2FV7)

Asymmetric Unit(hide GO term definitions)

Chain A,B (RBSK_HUMAN | Q9H477)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016773	phosphotransferase activity, alcohol group as acceptor	Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0004747	ribokinase activity	Catalysis of the reaction: ATP + D-ribose = ADP + D-ribose 5-phosphate.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0019303	D-ribose catabolic process	The chemical reactions and pathways resulting in the breakdown of D-ribose (ribo-pentose).
	GO:0006014	D-ribose metabolic process	The chemical reactions and pathways involving D-ribose (ribo-pentose). As beta-D-ribofuranose, D-ribose forms the glycose group of all ribonucleosides, ribonucleotides and ribonucleic acids, and also of ribose phosphates, various glycosides, some coenzymes and some forms of vitamin B12.
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0046835	carbohydrate phosphorylation	The process of introducing a phosphate group into a carbohydrate, any organic compound based on the general formula Cx(H2O)y.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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	Cis Peptide Bonds
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	2fv7
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	RBSK_HUMAN \| Q9H477	:	5byc 5byd 5bye 5byf 5c3y 5c3z 5c40 5c41

(no "Related Entries Specified in the PDB File" available for 2FV7)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 18)

Sites (15, 15)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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Exons (8, 16)

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