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Description

Title :   SOLUTION STRUCTURE OF THE SMR DOMAIN OF NEDD4-BINDING PROTEIN 2

Authors :   H. P. Zhang, C. Kurosaki, M. Yoshida, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   09 Dec 05 (Deposition) - 09 Jun 06 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Smr Domain, Nedd4-Binding Protein 2, N4Bp2, Bcl-3 Binding Protein, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Apoptosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. P. Zhang, C. Kurosaki, M. Yoshida, F. Hayashi, S. Yokoyama
Solution Structure Of The Smr Domain Of Nedd4-Binding Protein 2
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Molecule 1 - NEDD4-BINDING PROTEIN 2
	Chains	:	A
	EC Number	:	3.-.-.-
	Engineered	:	YES
	Expression System Plasmid	:	P050627-22
	Expression System Vector Type	:	PLASMID
	Fragment	:	SMR DOMAIN
	Gene	:	N4BP2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL FREE PROTEIN SYNTHESIS
	Synonym	:	N4BP2, BCL-3-BINDING PROTEIN

Structural Features

Chains, Units


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2D9I)

Sites (0, 0)

(no "Site" information available for 2D9I)

SS Bonds (0, 0)

(no "SS Bond" information available for 2D9I)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 2D9I)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 2D9I)

PROSITE Motifs (1, 1)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SMR	PS50828	Smr domain profile.	N4BP2_HUMAN	1691-1770	1	A:11-90

Exons (4, 4)

NMR Structure (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000261435	1a	ENSE00002042060	chr4:40058446-40058650	205	N4BP2_HUMAN	-	0	0	-	-
1.2	ENST00000261435	2	ENSE00001489911	chr4:40075075-40075171	97	N4BP2_HUMAN	-	0	0	-	-
1.3	ENST00000261435	3	ENSE00001077370	chr4:40098847-40099189	343	N4BP2_HUMAN	1-77	77	0	-	-
1.5b	ENST00000261435	5b	ENSE00001077368	chr4:40103695-40104838	1144	N4BP2_HUMAN	77-458	382	0	-	-
1.6	ENST00000261435	6	ENSE00001077366	chr4:40108520-40108644	125	N4BP2_HUMAN	458-500	43	0	-	-
1.7	ENST00000261435	7	ENSE00001077374	chr4:40113704-40113792	89	N4BP2_HUMAN	500-529	30	0	-	-
1.8	ENST00000261435	8	ENSE00001077367	chr4:40115052-40115128	77	N4BP2_HUMAN	530-555	26	0	-	-
1.9	ENST00000261435	9	ENSE00001077378	chr4:40119489-40119644	156	N4BP2_HUMAN	555-607	53	0	-	-
1.10	ENST00000261435	10	ENSE00001077376	chr4:40121552-40123929	2378	N4BP2_HUMAN	607-1400	794	0	-	-
1.11	ENST00000261435	11	ENSE00001077380	chr4:40124747-40124832	86	N4BP2_HUMAN	1400-1428	29	0	-	-
1.12	ENST00000261435	12	ENSE00001077375	chr4:40125780-40125825	46	N4BP2_HUMAN	1429-1444	16	0	-	-
1.13	ENST00000261435	13	ENSE00001077373	chr4:40127754-40127950	197	N4BP2_HUMAN	1444-1509	66	0	-	-
1.14	ENST00000261435	14	ENSE00001077371	chr4:40133421-40133539	119	N4BP2_HUMAN	1510-1549	40	0	-	-
1.15	ENST00000261435	15	ENSE00001035498	chr4:40138564-40138702	139	N4BP2_HUMAN	1549-1595	47	0	-	-
1.16a	ENST00000261435	16a	ENSE00001035492	chr4:40144293-40144481	189	N4BP2_HUMAN	1596-1658	63	1	A:1-6 (gaps)	12
1.17	ENST00000261435	17	ENSE00001035489	chr4:40146252-40146420	169	N4BP2_HUMAN	1659-1715	57	1	A:7-35 (gaps)	57
1.18	ENST00000261435	18	ENSE00001035496	chr4:40154400-40154523	124	N4BP2_HUMAN	1715-1756	42	1	A:35-76	42
1.19c	ENST00000261435	19c	ENSE00001860132	chr4:40155812-40159872	4061	N4BP2_HUMAN	1756-1770	15	1	A:76-90	15

Sequences/Alignments

NMR Structure

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:96
 aligned with N4BP2_HUMAN | Q86UW6 from UniProtKB/Swiss-Prot  Length:1770

    Alignment length:130
                                                                                                                                                    1770      
                                  1656      1666      1676      1686      1696      1706      1716      1726      1736      1746      1756      1766   |     -
         N4BP2_HUMAN   1647 GKKNVATFYAQQGTLHEQKMKEANHLAAIEIFEKVNASLLPQNVLDLHGLHVDEALEHLMRVLEKKTEEFKQNGGKPYLSVITGRGNHSQGGVARIKPAVIKYLISHSFRFSEIKPGCLKVMLK------    -
               SCOP domains -----------------------------------------d2d9ia1 A:8-90 Nedd4-binding protein 2                                             ------ SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...------....----------------------------..eee....hhhhhhhhhhhhhhhhhhhhhhh....eeeee...hhhhh....hhhhhhhhhhhhh...ee......eeee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------SMR  PDB: A:11-90 UniProt: 1691-1770                                            ------ PROSITE
           Transcript 1 (1) Exon 1.16a  Exon 1.17  PDB: A:7-35 (gaps) UniProt: 1659-1715         ----------------------------------------Exon 1.19c     ------ Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------Exon 1.18  PDB: A:35-76 UniProt: 1715-1756-------------------- Transcript 1 (2)
                2d9i A    1 GSS------GSSG----------------------------QNVLDLHGLHVDEALEHLMRVLEKKTEEFKQNGGKPYLSVITGRGNHSQGGVARIKPAVIKYLISHSFRFSEIKPGCLKVMLKSGPSSG   96
                              |      4  |      -         -         - |      16        26        36        46        56        66        76        86        96
                              3      4  7                            8

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: IF3-like (127)

Superfamily: SMR domain-like (2)

Family: Smr domain (2)

Protein domain: Nedd4-binding protein 2 (1)

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

d2d9ia1

A:8-90

CATH Domains (0, 0)

(no "CATH Domain" information available for 2D9I)

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 2D9I)

Gene Ontology (10, 10)

NMR Structure(hide GO term definitions)

Chain A (N4BP2_HUMAN | Q86UW6)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0046404	ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity	Catalysis of the reaction: ATP + 5'-dephospho-DNA = ADP + 5'-phospho-DNA.
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	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: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).
biological process
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
	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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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Related Entries

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	N4BP2_HUMAN \| Q86UW6	:	2vkc 3bhb 3fau

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