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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN SMALL-MUTS RELATED DOMAIN
 
Authors :  T. G. Kim, T. H. Kwon, E. K. Ryu, K. Min, S. -D. Heo, K. M. Song, W. J. Jun, E. Jung
Date :  18 Nov 08  (Deposition) - 15 Dec 09  (Release) - 15 Dec 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A (1x),D (1x)
Biol. Unit 3:  B,C  (1x)
Keywords :  Smr, Small-Muts Related Domain, Nicking Endonuclease, Alternative Splicing, Atp-Binding, Coiled Coil, Cytoplasm, Hydrolase, Nucleotide-Binding, Phosphoprotein, Polymorphism, Ubl Conjugation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. G. Kim, T. H. Kwon, C. Ban, J. K. Ku
Strcutral Dynamincs Of The Endonuclease Small-Muts Related Domains Of Bcl3 Binding Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NEDD4-BINDING PROTEIN 2
    Chains: A, B, C, D
    EC Number: 3.-.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: DNA BINDING DOMAIN
    Gene: B3BP, KIAA1413, N4BP2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Strain: HELA CDNA
    Synonym: N4BP2, BCL-3-BINDING PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): ABCD
Biological Unit 2 (1x): A (1x)  D (1x)
Biological Unit 3 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3FAU)

(-) Sites  (0, 0)

(no "Site" information available for 3FAU)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3FAU)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3FAU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FAU)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SMRPS50828 Smr domain profile.N4BP2_HUMAN1691-1770
 
 
 		  4A:11-89
B:11-90
C:11-89
D:11-90
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SMRPS50828 Smr domain profile.N4BP2_HUMAN1691-1770
 
 
 		  4A:11-89
B:11-90
C:11-89
D:11-90
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SMRPS50828 Smr domain profile.N4BP2_HUMAN1691-1770
 
 
 		  2A:11-89
-
-
D:11-90
Biological Unit 3 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SMRPS50828 Smr domain profile.N4BP2_HUMAN1691-1770
 
 
 		  2-
B:11-90
C:11-89
-

(-) Exons   (3, 12)

Asymmetric Unit (3, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002614351aENSE00002042060chr4:40058446-40058650205N4BP2_HUMAN-00--
1.2ENST000002614352ENSE00001489911chr4:40075075-4007517197N4BP2_HUMAN-00--
1.3ENST000002614353ENSE00001077370chr4:40098847-40099189343N4BP2_HUMAN1-77770--
1.5bENST000002614355bENSE00001077368chr4:40103695-401048381144N4BP2_HUMAN77-4583820--
1.6ENST000002614356ENSE00001077366chr4:40108520-40108644125N4BP2_HUMAN458-500430--
1.7ENST000002614357ENSE00001077374chr4:40113704-4011379289N4BP2_HUMAN500-529300--
1.8ENST000002614358ENSE00001077367chr4:40115052-4011512877N4BP2_HUMAN530-555260--
1.9ENST000002614359ENSE00001077378chr4:40119489-40119644156N4BP2_HUMAN555-607530--
1.10ENST0000026143510ENSE00001077376chr4:40121552-401239292378N4BP2_HUMAN607-14007940--
1.11ENST0000026143511ENSE00001077380chr4:40124747-4012483286N4BP2_HUMAN1400-1428290--
1.12ENST0000026143512ENSE00001077375chr4:40125780-4012582546N4BP2_HUMAN1429-1444160--
1.13ENST0000026143513ENSE00001077373chr4:40127754-40127950197N4BP2_HUMAN1444-1509660--
1.14ENST0000026143514ENSE00001077371chr4:40133421-40133539119N4BP2_HUMAN1510-1549400--
1.15ENST0000026143515ENSE00001035498chr4:40138564-40138702139N4BP2_HUMAN1549-1595470--
1.16aENST0000026143516aENSE00001035492chr4:40144293-40144481189N4BP2_HUMAN1596-1658630--
1.17ENST0000026143517ENSE00001035489chr4:40146252-40146420169N4BP2_HUMAN1659-1715574A:10-35
B:10-35
C:9-35
D:10-35		26
26
27
26
1.18ENST0000026143518ENSE00001035496chr4:40154400-40154523124N4BP2_HUMAN1715-1756424A:35-76 (gaps)
B:35-76
C:35-76 (gaps)
D:35-76 (gaps)		42
42
42
42
1.19cENST0000026143519cENSE00001860132chr4:40155812-401598724061N4BP2_HUMAN1756-1770154A:76-89
B:76-90
C:76-89
D:76-90		14
15
14
15

(-) Sequences/Alignments

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:71
 aligned with N4BP2_HUMAN | Q86UW6 from UniProtKB/Swiss-Prot  Length:1770

    Alignment length:80
                                  1699      1709      1719      1729      1739      1749      1759      1769
         N4BP2_HUMAN   1690 VLDLHGLHVDEALEHLMRVLEKKTEEFKQNGGKPYLSVITGRGNHSQGGVARIKPAVIKYLISHSFRFSEIKPGCLKVML 1769
               SCOP domains d3faua_ A: automated matches                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee....hhhhhhhhhhhhhhhhhhhhhhhh...eeeee...---------hhhhhhhhhhhhh...eeeee..eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -SMR  PDB: A:11-89 UniProt: 1691-1770                                            PROSITE
           Transcript 1 (1) Exon 1.17  PDB: A:10-35   ----------------------------------------Exon 1.19c     Transcript 1 (1)
           Transcript 1 (2) -------------------------Exon 1.18  PDB: A:35-76 (gaps)            ------------- Transcript 1 (2)
                3fau A   10 SLDLHGLHVDEALEHLMRVLEKKTEEFKQNGGKPYLSVITGR---------RIKPAVIKYLISHSFRFSEIKPGCLKVML   89
                                    19        29        39        49 |       - |      69        79        89
                                                                    51        61                            


Chain B from PDB  Type:PROTEIN  Length:81
 aligned with N4BP2_HUMAN | Q86UW6 from UniProtKB/Swiss-Prot  Length:1770

    Alignment length:81
                                  1699      1709      1719      1729      1739      1749      1759      1769 
         N4BP2_HUMAN   1690 VLDLHGLHVDEALEHLMRVLEKKTEEFKQNGGKPYLSVITGRGNHSQGGVARIKPAVIKYLISHSFRFSEIKPGCLKVMLK 1770
               SCOP domains d3faub_ B: automated matches                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee....hhhhhhhhhhhhhhhhhhhhhhh....eeeee......ee..eehhhhhhhhhhhhh...eeeee..eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -SMR  PDB: B:11-90 UniProt: 1691-1770                                             PROSITE
           Transcript 1 (1) Exon 1.17  PDB: B:10-35   ----------------------------------------Exon 1.19c      Transcript 1 (1)
           Transcript 1 (2) -------------------------Exon 1.18  PDB: B:35-76 UniProt: 1715-1756-------------- Transcript 1 (2)
                3fau B   10 SLDLHGLHVDEALEHLMRVLEKKTEEFKQNGGKPYLSVITGRGNHSQGGVARIKPAVIKYLISHSFRFSEIKPGCLKVMLK   90
                                    19        29        39        49        59        69        79        89 


Chain C from PDB  Type:PROTEIN  Length:77
 aligned with N4BP2_HUMAN | Q86UW6 from UniProtKB/Swiss-Prot  Length:1770

    Alignment length:81
                                  1698      1708      1718      1728      1738      1748      1758      1768 
         N4BP2_HUMAN   1689 NVLDLHGLHVDEALEHLMRVLEKKTEEFKQNGGKPYLSVITGRGNHSQGGVARIKPAVIKYLISHSFRFSEIKPGCLKVML 1769
               SCOP domains d3fauc_ C: automated matches                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee....hhhhhhhhhhhhhhhhhhhhhhhh...eeeee....----hhhhhhhhhhhhhhhhh...eeeee..eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --SMR  PDB: C:11-89 UniProt: 1691-1770                                            PROSITE
           Transcript 1 (1) Exon 1.17  PDB: C:9-35     ----------------------------------------Exon 1.19c     Transcript 1 (1)
           Transcript 1 (2) --------------------------Exon 1.18  PDB: C:35-76 (gaps)            ------------- Transcript 1 (2)
                3fau C    9 GSLDLHGLHVDEALEHLMRVLEKKTEEFKQNGGKPYLSVITGRG----GGVARIKPAVIKYLISHSFRFSEIKPGCLKVML   89
                                    18        28        38        48   |    58        68        78        88 
                                                                      52   57                                


Chain D from PDB  Type:PROTEIN  Length:79
 aligned with N4BP2_HUMAN | Q86UW6 from UniProtKB/Swiss-Prot  Length:1770

    Alignment length:81
                                  1699      1709      1719      1729      1739      1749      1759      1769 
         N4BP2_HUMAN   1690 VLDLHGLHVDEALEHLMRVLEKKTEEFKQNGGKPYLSVITGRGNHSQGGVARIKPAVIKYLISHSFRFSEIKPGCLKVMLK 1770
               SCOP domains d3faud_ D: automated matches                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee....hhhhhhhhhhhhhhhhhhhhhhh....eeeee....--......hhhhhhhhhhhhh...eee....eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -SMR  PDB: D:11-90 UniProt: 1691-1770                                             PROSITE
           Transcript 1 (1) Exon 1.17  PDB: D:10-35   ----------------------------------------Exon 1.19c      Transcript 1 (1)
           Transcript 1 (2) -------------------------Exon 1.18  PDB: D:35-76 (gaps)            -------------- Transcript 1 (2)
                3fau D   10 SLDLHGLHVDEALEHLMRVLEKKTEEFKQNGGKPYLSVITGRG--SQGGVARIKPAVIKYLISHSFRFSEIKPGCLKVMLK   90
                                    19        29        39        49  |  |  59        69        79        89 
                                                                     52 55
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3FAU)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FAU)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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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  3fau
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  N4BP2_HUMAN | Q86UW6
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        N4BP2_HUMAN | Q86UW6: 2d9i 2vkc 3bhb

(-) Related Entries Specified in the PDB File

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