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(-) Description

Title :  SWIRM DOMAIN OF HUMAN LSD1
 
Authors :  P. D. Jeffrey, P. Yuan
Date :  16 Mar 16  (Deposition) - 18 May 16  (Release) - 18 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Keywords :  Helix, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Hu, X. Sun, U. F. S. Hameed, B. S. Moorthy, P. D. Jeffrey, L. Zhou, X. Ma F. Chen, Q. Mu, J. Pei, K. Swaminathan, P. Yuan
A Tlx-Interacting Peptide Of Lsd1 Inhibits The Proliferatio Of Brain Tumor Stem Cells
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - LYSINE-SPECIFIC HISTONE DEMETHYLASE 1A
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI K-12
    Expression System Strain: K-12
    Expression System Taxid: 83333
    Fragment: SWIRM DOMAIN, UNP RESIDUES 183-267
    Gene: KDM1A, AOF2, KDM1, KIAA0601, LSD1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BRAF35-HDAC COMPLEX PROTEIN BHC110,FLAVIN-CONTAINING AMINE OXIDASE DOMAIN-CONTAINING PROTEIN 2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): A 
Biological Unit 2 (2x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU B:183 , HOH B:444 , HOH B:455 , HOH B:478 , HOH B:489binding site for residue MG B 301
2AC2SOFTWAREHOH B:412 , HOH B:424 , HOH B:426binding site for residue MG B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5IT3)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:240 -Pro A:241
2Ala B:240 -Pro B:241

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5IT3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5IT3)

(-) Exons   (0, 0)

(no "Exon" information available for 5IT3)

(-) 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:85
                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh.......hhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 5it3 A 183 LPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIY 267
                                   192       202       212       222       232       242       252       262     


Chain B from PDB  Type:PROTEIN  Length:85
                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh........hhhhhhhhhhhhhhh..hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 5it3 B 183 LPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIY 267
                                   192       202       212       222       232       242       252       262
   Legend:   → Mismatch (orange background)
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  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 5IT3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5IT3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5IT3)

(-) Gene Ontology  (66, 66)

Asymmetric Unit(hide GO term definitions)

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  KDM1A_HUMAN | O60341
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 Related Entries

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

UniProtKB/Swiss-Prot
        KDM1A_HUMAN | O60341: 2com 2dw4 2ejr 2h94 2hko 2iw5 2l3d 2uxn 2uxx 2v1d 2x0l 2xaf 2xag 2xah 2xaj 2xaq 2xas 2y48 2z3y 2z5u 3abt 3abu 3zms 3zmt 3zmu 3zmv 3zmz 3zn0 3zn1 4bay 4czz 4kum 4uv8 4uv9 4uva 4uvb 4uvc 4uxn 4xbf 5afw 5h6q 5h6r 5l3b 5l3c 5l3d 5l3e 5l3f 5l3g 5lbq 5lgn 5lgt 5lgu 5lhg 5lhh 5lhi 5x60

(-) Related Entries Specified in the PDB File

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