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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PRDM9 SET DOMAIN IN COMPLEX WITH H3K4ME2 AND ADOHCY.
 
Authors :  N. Mathioudakis, S. Cusack, J. Kadlec
Date :  13 Aug 13  (Deposition) - 16 Oct 13  (Release) - 06 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transferase-Peptide Complex, Histone Methyltransferase, Set Domain H3K4Me3, (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Wu, N. Mathioudakis, B. Diagouraga, A. Dong, L. Dombrovski, F. Baudat, S. Cusack, B. De Massy, J. Kadlec
Molecular Basis For The Regulation Of The H3K4 Methyltransferase Activity Of Prdm9.
Cell Rep. V. 5 13 2013
PubMed-ID: 24095733  |  Reference-DOI: 10.1016/J.CELREP.2013.08.035

(-) Compounds

Molecule 1 - HISTONE-LYSINE N-METHYLTRANSFERASE PRDM9
    ChainsA, B
    EC Number2.1.1.43
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPPROEXHTB
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantSTAR
    Expression System Vector TypePLASMID
    FragmentSET DOMAIN, RESIDUES 198-368
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymPRDM9, HYBRID STERILITY PROTEIN 1, MEIOSIS-INDUCED FACTOR CONTAINING A PR/SET DOMAIN AND ZINC-FINGER MO PR DOMAIN ZINC FINGER PROTEIN 9, PR DOMAIN-CONTAINING PROTEIN 9
 
Molecule 2 - HISTONE H3.1
    ChainsC
    FragmentN-TERMINUS, RESIDUES 2-11
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsDOUBLE METHYLATION ON LYSINE 4
    SynonymHISTONE H3, HISTONE H3/A, HISTONE H3/B, HISTONE H3/C, HISTON HISTONE H3/F, HISTONE H3/H, HISTONE H3/I, HISTONE H3/J, HISTONE H3/K, HISTONE H3/L
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A C
Biological Unit 2 (1x) B 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric Unit (4, 5)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MLY1Mod. Amino AcidN-DIMETHYL-LYSINE
3SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
4ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2MLY1Mod. Amino AcidN-DIMETHYL-LYSINE
3SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MLY-1Mod. Amino AcidN-DIMETHYL-LYSINE
3SAH-1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
4ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:253 , ALA A:256 , LEU A:258 , TYR A:291 , ARG A:317 , ASN A:320 , CYS A:321 , ARG A:323 , TYR A:357 , TYR A:361 , HOH A:2024 , HOH A:2035 , ARG C:2 , MLY C:4BINDING SITE FOR RESIDUE SAH A 394
2AC2SOFTWARECYS A:205 , CYS A:208 , CYS A:216 , HIS A:219BINDING SITE FOR RESIDUE ZN A 493
3AC3SOFTWARECYS B:205 , CYS B:208 , CYS B:216 , HIS B:219BINDING SITE FOR RESIDUE ZN B 493
4AC4SOFTWARETYR B:276 , GLY B:290 , SER B:292 , TRP B:293 , VAL B:319BINDING SITE FOR RESIDUE GOL B1358

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4C1Q)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:274 -Pro A:275
2Gly B:274 -Pro B:275

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4C1Q)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SETPS50280 SET domain profile.PRDM9_MOUSE244-358
 
  2A:244-358
B:244-357
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SETPS50280 SET domain profile.PRDM9_MOUSE244-358
 
  1A:244-358
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SETPS50280 SET domain profile.PRDM9_MOUSE244-358
 
  1-
B:244-357

(-) Exons   (1, 1)

Asymmetric Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2bENST000003593032bENSE00001974165chr6:27858570-27858160411H31_HUMAN1-1361361C:1-77

(-) 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:173
 aligned with PRDM9_MOUSE | Q96EQ9 from UniProtKB/Swiss-Prot  Length:843

    Alignment length:173
                                   204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364   
          PRDM9_MOUSE   195 SEPQDDDYLYCEKCQNFFIDSCPNHGPPLFVKDSMVDRGHPNHSVLSLPPGLRISPSGIPEAGLGVWNEASDLPVGLHFGPYEGQITEDEEAANSGYSWLITKGRNCYEYVDGQDESQANWMRYVNCARDDEEQNLVAFQYHRKIFYRTCRVIRPGCELLVWYGDEYGQELGI 367
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh...eee....eee...........ee..........hhhhhh....eeeee.......eeeee.........ee.....eee...hhhhh..eeeee.....eeeee.......hhhhhhee........eeeeee..eeeeee..........ee..hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------SET  PDB: A:244-358 UniProt: 244-358                                                                               --------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c1q A 195 AMSQDDDYLYCEKCQNFFIDSCPNHGPPLFVKDSMVDRGHPNHSVLSLPPGLRISPSGIPEAGLGVWNEASDLPVGLHFGPYEGQITEDEEAANSGYSWLITKGRNCYEYVDGQDESQANWMRYVNCARDDEEQNLVAFQYHRKIFYRTCRVIRPGCELLVWYGDEYGQELGI 367
                                   204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364   

Chain B from PDB  Type:PROTEIN  Length:162
 aligned with PRDM9_MOUSE | Q96EQ9 from UniProtKB/Swiss-Prot  Length:843

    Alignment length:164
                                   203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353    
          PRDM9_MOUSE   194 VSEPQDDDYLYCEKCQNFFIDSCPNHGPPLFVKDSMVDRGHPNHSVLSLPPGLRISPSGIPEAGLGVWNEASDLPVGLHFGPYEGQITEDEEAANSGYSWLITKGRNCYEYVDGQDESQANWMRYVNCARDDEEQNLVAFQYHRKIFYRTCRVIRPGCELLVWY 357
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..--.....eee....eee...........ee..........hhhhhh....eeeee.......eeeee.........ee.....eee...hhhhh..eeeee.....eeeee.......hhhhhhee........eeeeee..eeeeee..........eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------SET  PDB: B:244-357 UniProt: 244-358                                                                               PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c1q B 196 MS--QDDDYLYCEKCQNFFIDSCPNHGPPLFVKDSMVDRGHPNHSVLSLPPGLRISPSGIPEAGLGVWNEASDLPVGLHFGPYEGQITEDEEAANSGYSWLITKGRNCYEYVDGQDESQANWMRYVNCARDDEEQNLVAFQYHRKIFYRTCRVIRPGCELLVWY 357
                             |  |  203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353    
                           197  |                                                                                                                                                               
                              198                                                                                                                                                               

Chain C from PDB  Type:PROTEIN  Length:7
 aligned with H31_HUMAN | P68431 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:7
            H31_HUMAN     2 ARTKQTA   8
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ..ee... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
               Transcript 1 1.2b    Transcript 1
                 4c1q C   1 ARTkQTA   7
                               |   
                               |   
                               4-MLY

   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 4C1Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4C1Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4C1Q)

(-) Gene Ontology  (49, 52)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PRDM9_MOUSE | Q96EQ9)
molecular function
    GO:0042800    histone methyltransferase activity (H3-K4 specific)    Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 4) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 4). This reaction is the addition of a methyl group onto lysine at position 4 of the histone H3 protein.
    GO:0018024    histone-lysine N-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + histone L-lysine = S-adenosyl-L-homocysteine + histone N6-methyl-L-lysine. The methylation of peptidyl-lysine in histones forms N6-methyl-L-lysine, N6,N6-dimethyl-L-lysine and N6,N6,N6-trimethyl-L-lysine derivatives.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0010844    recombination hotspot binding    Interacting selectively and non-covalently with a region in a genome which promotes recombination.
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    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:0051568    histone H3-K4 methylation    The modification of histone H3 by addition of one or more methyl groups to lysine at position 4 of the histone.
    GO:0034968    histone lysine methylation    The modification of a histone by addition of one or more methyl groups to a lysine residue.
    GO:0016571    histone methylation    The modification of histones by addition of methyl groups.
    GO:0051321    meiotic cell cycle    Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions.
    GO:0006311    meiotic gene conversion    The cell cycle process in which genetic information is transferred from one helix to another. It often occurs in association with general genetic recombination events, and is believed to be a straightforward consequence of the mechanisms of general recombination and DNA repair. For example, meiosis might yield three copies of the maternal version of an allele and only one copy of the paternal allele, indicating that one of the two copies of the paternal allele has been changed to a copy of the maternal allele.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0060903    positive regulation of meiosis I    Any process that increases the rate, frequency, or extent of meiosis I, a cell cycle process comprising the steps by which a cell progresses through the first phase of meiosis, in which cells divide and homologous chromosomes are paired and segregated from each other, producing two daughter cells.
    GO:0010845    positive regulation of reciprocal meiotic recombination    Any process that increases the frequency, rate or extent of recombination during meiosis. Reciprocal meiotic recombination is the cell cycle process in which double strand breaks are formed and repaired through a double Holliday junction intermediate.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    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.

Chain C   (H31_HUMAN | P68431)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0042393    histone binding    Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
    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:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
    GO:0006335    DNA replication-dependent nucleosome assembly    The formation of nucleosomes on newly replicated DNA, coupled to strand elongation.
    GO:0007596    blood coagulation    The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
    GO:0044267    cellular protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
    GO:0000183    chromatin silencing at rDNA    Repression of transcription of ribosomal DNA by altering the structure of chromatin.
    GO:0031047    gene silencing by RNA    Any process in which RNA molecules inactivate expression of target genes.
    GO:0045814    negative regulation of gene expression, epigenetic    Any epigenetic process that stops, prevents or reduces the rate of gene expression.
    GO:0006334    nucleosome assembly    The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
    GO:0002230    positive regulation of defense response to virus by host    Any host process that results in the promotion of antiviral immune response mechanisms, thereby limiting viral replication.
    GO:0045815    positive regulation of gene expression, epigenetic    Any epigenetic process that activates or increases the rate of gene expression.
    GO:0051290    protein heterotetramerization    The formation of a protein heterotetramer, a macromolecular structure consisting of four noncovalently associated subunits, of which not all are identical.
    GO:0060968    regulation of gene silencing    Any process that modulates the rate, frequency, or extent of gene silencing, the transcriptional or post-transcriptional process carried out at the cellular level that results in long-term gene inactivation.
    GO:0032200    telomere organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of telomeres, terminal regions of a linear chromosome that include the telomeric DNA repeats and associated proteins.
    GO:0098792    xenophagy    The macroautophagy process in which a region of cytoplasm containing an intracellular pathogen or some part of an intracellular pathogen (e.g. viral capsid) is enclosed in a double membrane bound autophagosome, which then fuses with the lysosome leading to degradation of the contents.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0000228    nuclear chromosome    A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact.
    GO:0000784    nuclear chromosome, telomeric region    The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0000788    nuclear nucleosome    A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA in the nucleus into higher order structures.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0000786    nucleosome    A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
    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.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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

UniProtKB/Swiss-Prot
        H31_HUMAN | P684311cs9 1ct6 1guw 1o9s 1q3l 2b2t 2b2u 2b2v 2b2w 2c1j 2c1n 2cv5 2kwj 2kwk 2l75 2lbm 2m0o 2ndf 2ndg 2oq6 2ot7 2ox0 2ri7 2uxn 2v89 2vpg 2x0l 3a1b 3afa 3avr 3ayw 3aze 3azf 3azg 3azh 3azi 3azj 3azk 3azl 3azm 3azn 3b95 3kmt 3kqi 3lqi 3lqj 3o34 3o35 3o37 3qj6 3rig 3riy 3sou 3sow 3u31 3u3d 3u4s 3u5n 3u5o 3u5p 3uee 3uef 3uig 3uii 3uik 3v43 3w96 3w97 3w98 3w99 3wa9 3waa 3wkj 3x1s 3x1t 3x1u 3x1v 3zg6 3zvy 4a0j 4a0n 4a7j 4bd3 4f4u 4f56 4ft2 4ft4 4fwf 4hon 4i51 4l7x 4lk9 4lka 4llb 4lxl 4n4h 4qbq 4qbr 4qbs 4tn7 4u68 4up0 4uy4 4x3k 4y6l 4yhp 4yhz 4ym5 4ym6 4z0r 4z2m 5av5 5av6 5av8 5av9 5avb 5avc 5b24 5b2i 5b2j 5b31 5c11 5c13 5c3i 5cpi 5cpj 5cpk 5d6y 5dah 5fb0 5fb1 5ffv 5gse 5gsu 5gt0 5gt3 5gtc 5hjb 5hjc 5hjd 5hyn 5iql 5j3v 5j9s 5jhn 5jin 5jiy 5jj0 5jrg 5kjh 5kji 5kkl 5m5g 5svx 5svy 5t0k 5t0m 5t1g 5t1i 5t8r 5tbn 5tdr 5tdw 5v21 5v22 5va6

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4C1Q)