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(-) Description

Title :  CRYSTAL STRUCTURE OF CHROMODOMAIN OF CBX4 IN COMPLEX WITH INHIBITOR UNC3866
 
Authors :  Y. Liu, W. Tempel, J. R. Walker, J. I. Stuckey, B. M. Dickson, L. I. James, C. Bountra, C. H. Arrowsmith, A. M. Edwards, J. Min, Structural Genom Consortium (Sgc)
Date :  11 Nov 15  (Deposition) - 23 Dec 15  (Release) - 24 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.81
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Structural Genomics, Structural Genomics Consortium, Sgc, Transcription-Transcription Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. I. Stuckey, B. M. Dickson, N. Cheng, Y. Liu, J. L. Norris, S. H. Cholensky, W. Tempel, S. Qin, K. G. Huber, C. Sagum, K. Black, F. Li X. P. Huang, B. L. Roth, B. M. Baughman, G. Senisterra, S. G. Pattenden, M. Vedadi, P. J. Brown, M. T. Bedford, J. Min, C. H. Arrowsmith, L. I. James, S. V. Frye
A Cellular Chemical Probe Targeting The Chromodomains Of Polycomb Repressive Complex 1.
Nat. Chem. Biol. V. 12 180 2016
PubMed-ID: 26807715  |  Reference-DOI: 10.1038/NCHEMBIO.2007

(-) Compounds

Molecule 1 - E3 SUMO-PROTEIN LIGASE CBX4
    Chains: A, B
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A-LIC
    Expression System Strain: BL21(DE3)-V2R-PRARE2
    Expression System Taxid: 562
    Gene: CBX4
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CHROMOBOX PROTEIN HOMOLOG 4,POLYCOMB 2 HOMOLOG,HPC2
 
Molecule 2 - UNC3866
    Chains: C, D
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: SYNTHETIC
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

Asymmetric Unit (4, 14)
No.NameCountTypeFull Name
15R02Mod. Amino Acid4-~{TERT}-BUTYLBENZOIC ACID
25R52Mod. Amino AcidMETHYL (2~{S})-2-AZANYL-3-OXIDANYL-PROPANOATE
3ELY2Mod. Amino AcidN~6~,N~6~-DIETHYL-L-LYSINE
4UNX8Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 1 (4, 6)
No.NameCountTypeFull Name
15R01Mod. Amino Acid4-~{TERT}-BUTYLBENZOIC ACID
25R51Mod. Amino AcidMETHYL (2~{S})-2-AZANYL-3-OXIDANYL-PROPANOATE
3ELY1Mod. Amino AcidN~6~,N~6~-DIETHYL-L-LYSINE
4UNX3Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 2 (4, 8)
No.NameCountTypeFull Name
15R01Mod. Amino Acid4-~{TERT}-BUTYLBENZOIC ACID
25R51Mod. Amino AcidMETHYL (2~{S})-2-AZANYL-3-OXIDANYL-PROPANOATE
3ELY1Mod. Amino AcidN~6~,N~6~-DIETHYL-L-LYSINE
4UNX5Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:9 , VAL A:10 , PHE A:11 , ALA A:12 , VAL A:13 , TRP A:32 , TRP A:35 , GLU A:43 , ASN A:47 , LEU A:49 , ASP A:50 , ARG A:52 , LEU A:53 , HOH A:212 , HOH A:216 , ALA B:12 , HOH C:201 , HOH C:202 , HOH C:203binding site for UNC3866 chain C
2AC2SOFTWAREGLU A:8 , HIS A:9 , LEU A:49 , PRO A:51 , HIS B:9 , VAL B:10 , PHE B:11 , ALA B:12 , VAL B:13 , TRP B:32 , TRP B:35 , TYR B:39 , GLU B:43 , ASN B:47 , LEU B:49 , ASP B:50 , ARG B:52 , LEU B:53 , HOH B:212 , HOH B:231 , HOH D:201 , HOH D:202binding site for UNC3866 chain D

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5EPL)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5EPL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EPL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5EPL)

(-) Exons   (0, 0)

(no "Exon" information available for 5EPL)

(-) 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:54
                                                                                     
               SCOP domains ------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee.eeeeeeeeee..eeeeeeee...hhhhheeee.hhh.hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------ Transcript
                  5epl A  6 GSEHVFAVESIEKKRIRKGRVEYLVKWRGWSPKYNTWEPEENILDPRLLIAFQN 59
                                    15        25        35        45        55    


Chain B from PDB  Type:PROTEIN  Length:58
                                                                                         
               SCOP domains ---------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author hhh.ee.eeeeeeeeee..eeeeeeee...hhhhheeee.hhh..hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                  5epl B  6 GSEHVFAVESIEKKRIRKGRVEYLVKWRGWSPKYNTWEPEENILDPRLLIAFQNRERQ 63
                                    15        25        35        45        55        


Chain C from PDB  Type:PROTEIN  Length:6
                                     
               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 ------ Transcript
                  5epl C  0 xFALxx  5
                            |   ||
                            0-5R0|
                                4-ELY
                                 5-5R5


Chain D from PDB  Type:PROTEIN  Length:6
                                     
               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 ------ Transcript
                  5epl D  0 xFALxx  5
                            |   ||
                            |   ||
                            0-5R0|
                                4-ELY
                                 5-5R5
   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 5EPL)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EPL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5EPL)

(-) Gene Ontology  (23, 23)

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  5epl
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  CBX4_HUMAN | O00257
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  6.3.2.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        CBX4_HUMAN | O00257: 2k28 3i8z

(-) Related Entries Specified in the PDB File

5epj 5epk 5eq0