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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE ING4 DIMERIZATION DOMAIN REVEALS THE FUNCTIONAL ORGANIZATION OF THE ING FAMILY OF CHROMATIN BINDING PROTEINS.
 
Authors :  S. Culurgioni, I. G. Munoz, A. Moreno, A. Palacios, M. Villate, I. Palme G. Montoya, F. J. Blanco
Date :  19 Jan 12  (Deposition) - 22 Feb 12  (Release) - 11 Jul 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.28
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,F  (1x)
Biol. Unit 3:  D,E  (1x)
Keywords :  Cell Cycle, Tumour Suppressor, Chromatin Remodelling (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Culurgioni, I. G. Munoz, A. Moreno, A. Palacios, M. Villate, I. Palmero, G. Montoya, F. J. Blanco
Crystal Structure Of Inhibitor Of Growth 4 (Ing4) Dimerization Domain Reveals Functional Organization Of Ing Family Of Chromatin-Binding Proteins.
J. Biol. Chem. V. 287 10876 2012
PubMed-ID: 22334692  |  Reference-DOI: 10.1074/JBC.M111.330001

(-) Compounds

Molecule 1 - INHIBITOR OF GROWTH PROTEIN 4
    ChainsA, B, C, D, E, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET11D
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL DIMERIZATION DOMAIN, RESIDUES 2-105
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymP29ING4

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)A C   
Biological Unit 2 (1x) B   F
Biological Unit 3 (1x)   DE 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 29)

Asymmetric Unit (1, 29)
No.NameCountTypeFull Name
1MSE29Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 9)
No.NameCountTypeFull Name
1MSE9Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 4AFL)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4AFL)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Tyr F:10 -Leu F:11

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AFL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4AFL)

(-) Exons   (4, 24)

Asymmetric Unit (4, 24)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000003968071cENSE00001945605chr12:6772306-677223176ING4_HUMAN1-13136A:3-13
B:4-13
C:4-13
D:5-13
E:4-13
F:10-13
11
10
10
9
10
4
1.7aENST000003968077aENSE00000866946chr12:6765964-676589372ING4_HUMAN13-37256A:13-37
B:13-37
C:13-37
D:13-37
E:13-37
F:13-37
25
25
25
25
25
25
1.9bENST000003968079bENSE00000715744chr12:6762562-6762396167ING4_HUMAN37-92566A:37-92
B:37-92
C:37-92
D:37-92 (gaps)
E:37-92
F:37-92 (gaps)
56
56
56
56
56
56
1.10bENST0000039680710bENSE00001789862chr12:6762216-6762102115ING4_HUMAN93-131396A:93-104
B:93-101
C:93-105
D:93-103
E:93-104
F:93-103
12
9
13
11
12
11
1.10dENST0000039680710dENSE00001526324chr12:6761936-6761828109ING4_HUMAN131-167370--
1.10iENST0000039680710iENSE00001721883chr12:6761584-6761437148ING4_HUMAN167-216500--
1.11bENST0000039680711bENSE00001640958chr12:6760551-676049062ING4_HUMAN217-237210--
1.11nENST0000039680711nENSE00001876036chr12:6760400-6759757644ING4_HUMAN237-249130--

(-) 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:102
 aligned with ING4_HUMAN | Q9UNL4 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:102
                                    12        22        32        42        52        62        72        82        92       102  
           ING4_HUMAN     3 AGMYLEHYLDSIENLPFELQRNFQLMRDLDQRTEDLKAEIDKLATEYMSSARSLSSEEKLALLKQIQEAYGKCKEFGDDKVQLAMQTYEMVDKHIRRLDTDL 104
               SCOP domains ------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1c  -----------------------Exon 1.9b  PDB: A:37-92 UniProt: 37-92                  Exon 1.10b   Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.7a  PDB: A:13-37  ------------------------------------------------------------------- Transcript 1 (2)
                 4afl A   3 AGmYLEHYLDSIENLPFELQRNFQLmRDLDQRTEDLKAEIDKLATEYmSSARSLSSEEKLALLKQIQEAYGKCKEFGDDKVQLAmQTYEmVDKHIRRLDTDL 104
                              |     12        22     |  32        42       |52        62        72        82    |   92       102  
                              |                     28-MSE                50-MSE                               87-MSE|            
                              5-MSE                                                                                 92-MSE        

Chain B from PDB  Type:PROTEIN  Length:98
 aligned with ING4_HUMAN | Q9UNL4 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:98
                                    13        23        33        43        53        63        73        83        93        
           ING4_HUMAN     4 GMYLEHYLDSIENLPFELQRNFQLMRDLDQRTEDLKAEIDKLATEYMSSARSLSSEEKLALLKQIQEAYGKCKEFGDDKVQLAMQTYEMVDKHIRRLD 101
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1c -----------------------Exon 1.9b  PDB: B:37-92 UniProt: 37-92                  1.10b     Transcript 1 (1)
           Transcript 1 (2) ---------Exon 1.7a  PDB: B:13-37  ---------------------------------------------------------------- Transcript 1 (2)
                 4afl B   4 GmYLEHYLDSIENLPFELQRNFQLmRDLDQRTEDLKAEIDKLATEYmSSARSLSSEEKLALLKQIQEAYGKCKEFGDDKVQLAmQTYEmVDKHIRRLD 101
                             |      13        23    |   33        43      | 53        63        73        83   |    93        
                             5-MSE                 28-MSE                50-MSE                               87-MSE|         
                                                                                                                   92-MSE     

Chain C from PDB  Type:PROTEIN  Length:102
 aligned with ING4_HUMAN | Q9UNL4 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:102
                                    13        23        33        43        53        63        73        83        93       103  
           ING4_HUMAN     4 GMYLEHYLDSIENLPFELQRNFQLMRDLDQRTEDLKAEIDKLATEYMSSARSLSSEEKLALLKQIQEAYGKCKEFGDDKVQLAMQTYEMVDKHIRRLDTDLA 105
               SCOP domains ------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1c -----------------------Exon 1.9b  PDB: C:37-92 UniProt: 37-92                  Exon 1.10b    Transcript 1 (1)
           Transcript 1 (2) ---------Exon 1.7a  PDB: C:13-37  -------------------------------------------------------------------- Transcript 1 (2)
                 4afl C   4 GmYLEHYLDSIENLPFELQRNFQLmRDLDQRTEDLKAEIDKLATEYmSSARSLSSEEKLALLKQIQEAYGKCKEFGDDKVQLAmQTYEmVDKHIRRLDTDLA 105
                             |      13        23    |   33        43      | 53        63        73        83   |    93       103  
                             5-MSE                 28-MSE                50-MSE                               87-MSE|             
                                                                                                                   92-MSE         

Chain D from PDB  Type:PROTEIN  Length:95
 aligned with ING4_HUMAN | Q9UNL4 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:99
                                    14        24        34        44        54        64        74        84        94         
           ING4_HUMAN     5 MYLEHYLDSIENLPFELQRNFQLMRDLDQRTEDLKAEIDKLATEYMSSARSLSSEEKLALLKQIQEAYGKCKEFGDDKVQLAMQTYEMVDKHIRRLDTD 103
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.----...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1c-----------------------Exon 1.9b  PDB: D:37-92 (gaps) UniProt: 37-92           Exon 1.10b  Transcript 1 (1)
           Transcript 1 (2) --------Exon 1.7a  PDB: D:13-37  ------------------------------------------------------------------ Transcript 1 (2)
                 4afl D   5 mYLEHYLDSIENLPFELQRNFQLmRDLDQRTEDLKAEIDKLATEYmS----LSSEEKLALLKQIQEAYGKCKEFGDDKVQLAmQTYEmVDKHIRRLDTD 103
                            |       14        24   |    34        44     ||  - |      64        74        84  |    |94         
                            5-MSE                 28-MSE                50-MSE56                             87-MSE|           
                                                                         51                                       92-MSE       

Chain E from PDB  Type:PROTEIN  Length:101
 aligned with ING4_HUMAN | Q9UNL4 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:101
                                    13        23        33        43        53        63        73        83        93       103 
           ING4_HUMAN     4 GMYLEHYLDSIENLPFELQRNFQLMRDLDQRTEDLKAEIDKLATEYMSSARSLSSEEKLALLKQIQEAYGKCKEFGDDKVQLAMQTYEMVDKHIRRLDTDL 104
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1c -----------------------Exon 1.9b  PDB: E:37-92 UniProt: 37-92                  Exon 1.10b   Transcript 1 (1)
           Transcript 1 (2) ---------Exon 1.7a  PDB: E:13-37  ------------------------------------------------------------------- Transcript 1 (2)
                 4afl E   4 GmYLEHYLDSIENLPFELQRNFQLmRDLDQRTEDLKAEIDKLATEYmSSARSLSSEEKLALLKQIQEAYGKCKEFGDDKVQLAmQTYEmVDKHIRRLDTDL 104
                             |      13        23    |   33        43      | 53        63        73        83   |    93       103 
                             5-MSE                 28-MSE                50-MSE                               87-MSE|            
                                                                                                                   92-MSE        

Chain F from PDB  Type:PROTEIN  Length:91
 aligned with ING4_HUMAN | Q9UNL4 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:94
                                    19        29        39        49        59        69        79        89        99    
           ING4_HUMAN    10 YLDSIENLPFELQRNFQLMRDLDQRTEDLKAEIDKLATEYMSSARSLSSEEKLALLKQIQEAYGKCKEFGDDKVQLAMQTYEMVDKHIRRLDTD 103
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.---.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.1c-----------------------Exon 1.9b  PDB: F:37-92 (gaps) UniProt: 37-92           Exon 1.10b  Transcript 1 (1)
           Transcript 1 (2) ---Exon 1.7a  PDB: F:13-37  ------------------------------------------------------------------ Transcript 1 (2)
                 4afl F  10 YLDSIENLPFELQRNFQLmRDLDQRTEDLKAEIDKLATEYmSS---LSSEEKLALLKQIQEAYGKCKEFGDDKVQLAmQTYEmVDKHIRRLDTD 103
                                    19        29        39        49| |   | 59        69        79       |89  |     99    
                                             28-MSE                50-MSE56                             87-MSE|           
                                                                     52                                      92-MSE       

   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  (0, 0)

(no "SCOP Domain" information available for 4AFL)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AFL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AFL)

(-) Gene Ontology  (24, 24)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (ING4_HUMAN | Q9UNL4)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0035064    methylated histone binding    Interacting selectively and non-covalently with a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
    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:0003713    transcription coactivator activity    Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006978    DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator    A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, resulting in the induction of the transcription of p21 (also known as WAF1, CIP1 and SDI1) or any equivalent protein, in response to the detection of DNA damage.
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0007050    cell cycle arrest    A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M).
    GO:0043966    histone H3 acetylation    The modification of histone H3 by the addition of an acetyl group.
    GO:0043983    histone H4-K12 acetylation    The modification of histone H4 by the addition of an acetyl group to a lysine residue at position 12 of the histone.
    GO:0043984    histone H4-K16 acetylation    The modification of histone H4 by the addition of an acetyl group to a lysine residue at position 16 of the histone.
    GO:0043981    histone H4-K5 acetylation    The modification of histone H4 by the addition of an acetyl group to a lysine residue at position 5 of the histone.
    GO:0043982    histone H4-K8 acetylation    The modification of histone H4 by the addition of an acetyl group to a lysine residue at position 8 of the histone.
    GO:0016573    histone acetylation    The modification of a histone by the addition of an acetyl group.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0045926    negative regulation of growth    Any process that stops, prevents or reduces the rate or extent of growth, the increase in size or mass of all or part of an organism.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0006473    protein acetylation    The addition of an acetyl group to a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid.
cellular component
    GO:0000123    histone acetyltransferase complex    A protein complex that possesses histone acetyltransferase activity.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        ING4_HUMAN | Q9UNL42k1j 2m1r 2pnx 2vnf

(-) Related Entries Specified in the PDB File

2vnf MOLECULAR BASIS OF HISTONE H3K4ME3 RECOGNITION BY ING4