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(-) Description

Title :  CRYSTAL STRUCTURE OF EMSY-HP1 COMPLEX
 
Authors :  Y. Huang
Date :  09 Jan 06  (Deposition) - 23 May 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A,B,C,D,E  (2x)
Keywords :  Ent Domain, Chromo Shadow Domain, Emsy Protein, Heterochromatin Protein 1, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Huang, M. P. Myers, R. M. Xu
Crystal Structure Of The Hp1-Emsy Complex Reveals An Unusua Mode Of Hp1 Binding.
Structure V. 14 703 2006
PubMed-ID: 16615912  |  Reference-DOI: 10.1016/J.STR.2006.01.007

(-) Compounds

Molecule 1 - PROTEIN EMSY
    ChainsE
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPGEX-KG
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL DOMAIN
    GeneEMSY, C11ORF30
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - CHROMOBOX PROTEIN HOMOLOG 1
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentCHROMO SHADOW DOMAIN
    GeneCBX1, CBX
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHETEROCHROMATIN PROTEIN 1 HOMOLOG BETA, HP1 BETA, MODIFIER 1 PROTEIN, M31, HETEROCHROMATIN PROTEIN P25, HP1HSBETA, P25BETA

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit ABCDE
Biological Unit 1 (2x)ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1SO48Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:155 , CYS A:156 , PRO A:157 , GLN A:158 , VAL A:159 , HOH A:621 , HOH A:626 , HOH A:665 , HOH A:666 , HOH A:669BINDING SITE FOR RESIDUE SO4 A 601
2AC2SOFTWAREHOH C:674 , LYS D:155 , CYS D:156 , PRO D:157 , GLN D:158 , VAL D:159 , HOH D:633 , HOH D:634 , HOH D:635 , HOH D:652BINDING SITE FOR RESIDUE SO4 D 602
3AC3SOFTWARELYS C:155 , CYS C:156 , PRO C:157 , GLN C:158 , VAL C:159 , HOH C:678BINDING SITE FOR RESIDUE SO4 C 603
4AC4SOFTWARELYS B:155 , CYS B:156 , PRO B:157 , GLN B:158 , VAL B:159 , HOH B:635BINDING SITE FOR RESIDUE SO4 B 604

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 5)

Asymmetric Unit (2, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ENTPS51138 EMSY N-terminal (ENT) domain profile.EMSY_HUMAN16-100  1E:16-100
2CHROMO_2PS50013 Chromo and chromo shadow domain profile.CBX1_HUMAN21-79
117-175
 
 
 
  4-
A:117-175
B:117-175
C:117-175
D:117-175
Biological Unit 1 (2, 10)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ENTPS51138 EMSY N-terminal (ENT) domain profile.EMSY_HUMAN16-100  2E:16-100
2CHROMO_2PS50013 Chromo and chromo shadow domain profile.CBX1_HUMAN21-79
117-175
 
 
 
  8-
A:117-175
B:117-175
C:117-175
D:117-175

(-) Exons   (6, 12)

Asymmetric Unit (6, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000003347361cENSE00001386178chr11:76156069-76156172104EMSY_HUMAN-00--
1.2aENST000003347362aENSE00002183521chr11:76157944-76158052109EMSY_HUMAN1-24241E:7-2418
1.3ENST000003347363ENSE00001223548chr11:76162902-76163001100EMSY_HUMAN24-57341E:24-5734
1.4aENST000003347364aENSE00002152029chr11:76164358-7616443275EMSY_HUMAN57-82261E:57-8226
1.6bENST000003347366bENSE00001696572chr11:76169227-76169402176EMSY_HUMAN82-141601E:82-12443
1.6eENST000003347366eENSE00001102458chr11:76170980-76171129150EMSY_HUMAN141-191510--
1.7ENST000003347367ENSE00001697568chr11:76174865-76175124260EMSY_HUMAN191-277870--
1.8ENST000003347368ENSE00001718146chr11:76183608-76183884277EMSY_HUMAN278-370930--
1.9aENST000003347369aENSE00001152940chr11:76207259-76207513255EMSY_HUMAN370-455860--
1.10aENST0000033473610aENSE00001102425chr11:76224430-76224579150EMSY_HUMAN455-505510--
1.11bENST0000033473611bENSE00001102392chr11:76227186-76227356171EMSY_HUMAN505-562580--
1.12ENST0000033473612ENSE00001102435chr11:76234199-76234335137EMSY_HUMAN562-607460--
1.13aENST0000033473613aENSE00001102384chr11:76237506-76237679174EMSY_HUMAN608-665580--
1.14ENST0000033473614ENSE00001102400chr11:76239312-76239510199EMSY_HUMAN666-732670--
1.15ENST0000033473615ENSE00001152902chr11:76246939-76247103165EMSY_HUMAN732-787560--
1.16ENST0000033473616ENSE00001102418chr11:76248839-76248994156EMSY_HUMAN787-839530--
1.17ENST0000033473617ENSE00001152894chr11:76250643-7625068442EMSY_HUMAN839-853150--
1.18cENST0000033473618cENSE00001152887chr11:76253260-76253411152EMSY_HUMAN853-903510--
1.19cENST0000033473619cENSE00001040003chr11:76255303-76255866564EMSY_HUMAN904-10911880--
1.20aENST0000033473620aENSE00001040001chr11:76256841-76257341501EMSY_HUMAN1092-12581670--
1.22fENST0000033473622fENSE00001403769chr11:76260996-762625861591EMSY_HUMAN1259-1322640--

2.2ENST000003934082ENSE00001515177chr17:46178560-46178117444CBX1_HUMAN-00--
2.5ENST000003934085ENSE00002178956chr17:46154403-46154227177CBX1_HUMAN1-47470--
2.6aENST000003934086aENSE00000735652chr17:46153540-46153363178CBX1_HUMAN47-106600--
2.7bENST000003934087bENSE00000735651chr17:46152462-4615236895CBX1_HUMAN107-138324A:108-138
B:109-138
C:109-138
D:110-138
31
30
30
29
2.8cENST000003934088cENSE00001824299chr17:46148941-461474141528CBX1_HUMAN138-185484A:138-175
B:138-175
C:138-175
D:138-175
38
38
38
38

(-) 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:68
 aligned with CBX1_HUMAN | P83916 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:68
                                   117       127       137       147       157       167        
           CBX1_HUMAN   108 EKPRGFARGLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERLTWHSYPS 175
               SCOP domains d2fmma_ A: Heterochromatin protein 1, HP1                            SCOP domains
               CATH domains 2fmmA00 A:108-175  [code=2.40.50.40, no name defined]                CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh..eeeeeeeeee..eeeeeeee......eeeehhhhhhhhhhhhhhhhhh.eee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------------------------------------------- PROSITE (2)
                PROSITE (1) ---------CHROMO_2  PDB: A:117-175 UniProt: 117-175                   PROSITE (1)
           Transcript 2 (1) Exon 2.7b  PDB: A:108-138      ------------------------------------- Transcript 2 (1)
           Transcript 2 (2) ------------------------------Exon 2.8c  PDB: A:138-175 [INCOMPLETE] Transcript 2 (2)
                 2fmm A 108 EKPRGFARGLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERLTWHSYPS 175
                                   117       127       137       147       157       167        

Chain B from PDB  Type:PROTEIN  Length:67
 aligned with CBX1_HUMAN | P83916 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:67
                                   118       128       138       148       158       168       
           CBX1_HUMAN   109 KPRGFARGLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERLTWHSYPS 175
               SCOP domains d2fmmb_ B: Heterochromatin protein 1, HP1                           SCOP domains
               CATH domains 2fmmB00 B:109-175  [code=2.40.50.40, no name defined]               CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh..eeeeeeee......eeeeee.....eeeeehhhhhhhhhhhhhhhhhh.eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------- PROSITE (2)
                PROSITE (1) --------CHROMO_2  PDB: B:117-175 UniProt: 117-175                   PROSITE (1)
           Transcript 2 (1) Exon 2.7b  PDB: B:109-138     ------------------------------------- Transcript 2 (1)
           Transcript 2 (2) -----------------------------Exon 2.8c  PDB: B:138-175 [INCOMPLETE] Transcript 2 (2)
                 2fmm B 109 KPRGFARGLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERLTWHSYPS 175
                                   118       128       138       148       158       168       

Chain C from PDB  Type:PROTEIN  Length:67
 aligned with CBX1_HUMAN | P83916 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:67
                                   118       128       138       148       158       168       
           CBX1_HUMAN   109 KPRGFARGLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERLTWHSYPS 175
               SCOP domains d2fmmc_ C: Heterochromatin protein 1, HP1                           SCOP domains
               CATH domains 2fmmC00 C:109-175  [code=2.40.50.40, no name defined]               CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh..eeeeeeee......eeeeee......eeeehhhhhhhhhhhhhhhhhh.eeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------- PROSITE (2)
                PROSITE (1) --------CHROMO_2  PDB: C:117-175 UniProt: 117-175                   PROSITE (1)
           Transcript 2 (1) Exon 2.7b  PDB: C:109-138     ------------------------------------- Transcript 2 (1)
           Transcript 2 (2) -----------------------------Exon 2.8c  PDB: C:138-175 [INCOMPLETE] Transcript 2 (2)
                 2fmm C 109 KPRGFARGLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERLTWHSYPS 175
                                   118       128       138       148       158       168       

Chain D from PDB  Type:PROTEIN  Length:66
 aligned with CBX1_HUMAN | P83916 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:66
                                   119       129       139       149       159       169      
           CBX1_HUMAN   110 PRGFARGLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERLTWHSYPS 175
               SCOP domains d2fmmd_ D: Heterochromatin protein 1, HP1                          SCOP domains
               CATH domains 2fmmD00 D:110-175  [code=2.40.50.40, no name defined]              CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhh..eeeeeeee......eeeeee......eeeehhhhhhhhhhhhhhhhhhhhee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------ PROSITE (2)
                PROSITE (1) -------CHROMO_2  PDB: D:117-175 UniProt: 117-175                   PROSITE (1)
           Transcript 2 (1) Exon 2.7b  PDB: D:110-138    ------------------------------------- Transcript 2 (1)
           Transcript 2 (2) ----------------------------Exon 2.8c  PDB: D:138-175 [INCOMPLETE] Transcript 2 (2)
                 2fmm D 110 PRGFARGLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERLTWHSYPS 175
                                   119       129       139       149       159       169      

Chain E from PDB  Type:PROTEIN  Length:118
 aligned with EMSY_HUMAN | Q7Z589 from UniProtKB/Swiss-Prot  Length:1322

    Alignment length:118
                                    16        26        36        46        56        66        76        86        96       106       116        
           EMSY_HUMAN     7 TLLDLSRDECKRILRKLELEAYAGVISALRAQGDLTKEKKDLLGELSKVLSISTERHRAEVRRAVNDERLTTIAHNMSGPNSSSEWSIEGRRLVPLMPRLVPQTAFTVTANAVANAAI 124
               SCOP domains --d2fmme1 E:9-124 Emsy                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh.eeeeee...hhhh.eeeee......ee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------ENT  PDB: E:16-100 UniProt: 16-100                                                   ------------------------ PROSITE
           Transcript 1 (1) Exon 1.2a         --------------------------------Exon 1.4a  PDB: E:57-82   ------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) -----------------Exon 1.3  PDB: E:24-57            ------------------------Exon 1.6b  PDB: E:82-124 UniProt: 82-141    Transcript 1 (2)
                 2fmm E   7 GPLDLSRDECKRILRKLELEAYAGVISALRAQGDLTKEKKDLLGELSKVLSISTERHRAEVRRAVNDERLTTIAHNMSGPNSSSEWSIEGRRLVPLMPRLVPQTAFTVTANAVANAAI 124
                                    16        26        36        46        56        66        76        86        96       106       116        

   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  (2, 5)

Asymmetric Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 25)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (CBX1_HUMAN | P83916)
molecular function
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:1990226    histone methyltransferase binding    Interacting selectively and non-covalently with a histone methyltransferase enzyme.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    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.
cellular component
    GO:0000785    chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.
    GO:0010369    chromocenter    A region in which centric, heterochromatic portions of one or more chromosomes form a compact structure.
    GO:0000775    chromosome, centromeric region    The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
    GO:0001939    female pronucleus    The pronucleus originating from the ovum that is being fertilized.
    GO:0001940    male pronucleus    The pronucleus originating from the spermatozoa that was involved in fertilization.
    GO:0000784    nuclear chromosome, telomeric region    The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0005720    nuclear heterochromatin    A condensed form of chromatin, occurring in the nucleus during interphase, that stains strongly with basophilic dyes. The DNA of heterochromatin is typically replicated at a later stage in the cell-division cycle than euchromatin.
    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.
    GO:0005721    pericentric heterochromatin    Heterochromatin that is located adjacent to the CENP-A rich centromere 'central core' and characterized by the modified histone H3K9me3.
    GO:0005819    spindle    The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart.

Chain E   (EMSY_HUMAN | Q7Z589)
molecular function
    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:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    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
        CBX1_HUMAN | P839161guw 1s4z 3f2u 3q6s 5t1g
        EMSY_HUMAN | Q7Z5891utu 1uz3

(-) Related Entries Specified in the PDB File

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