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(-) Description

Title :  CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY WITH S21056A
 
Authors :  V. Srikannathasan, C. Gileadi, C. Johansson, T. Krojer, A. Tumber, F. V C. H. Arrowsmith, C. Bountra, A. Edwards, P. Brennan, U. Oppermann
Date :  01 May 15  (Deposition) - 17 Jun 15  (Release) - 17 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Srikannathasan, C. Gileadi, C. Johansson, T. Krojer, A. Tumber, F. Von Delft, C. H. Arrowsmith, C. Bountra, A. Edwards, P. Brennan, U. Oppermann
Crystal Structure Of Jmjc Domain Of Human Histone Demethylase Uty With S21056A
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UBIQUITOUSLY TRANSCRIBED TETRATRICOPEPTIDE REPEAT PROTEIN Y-LINKED TRANSCRIPT VARIANT 57
    Cell Line: SF9
    Chains: A, B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Fragment: JMJC DOMAIN, RESIDUES 799-1268
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HISTONE DEMETHYLASE UTY

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 17)

Asymmetric Unit (4, 17)
No.NameCountTypeFull Name
1EDO11Ligand/Ion1,2-ETHANEDIOL
2FE22Ligand/IonFE (II) ION
3S2I2Ligand/Ion3-[[2-PYRIDIN-2-YL-6-(1,2,4,5-TETRAHYDRO-3-BENZAZEPIN-3-YL)PYRIMIDIN-4-YL]AMINO]PROPAN-1-OL
4ZN2Ligand/IonZINC ION
Biological Unit 1 (3, 11)
No.NameCountTypeFull Name
1EDO9Ligand/Ion1,2-ETHANEDIOL
2FE21Ligand/IonFE (II) ION
3S2I1Ligand/Ion3-[[2-PYRIDIN-2-YL-6-(1,2,4,5-TETRAHYDRO-3-BENZAZEPIN-3-YL)PYRIMIDIN-4-YL]AMINO]PROPAN-1-OL
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2FE21Ligand/IonFE (II) ION
3S2I1Ligand/Ion3-[[2-PYRIDIN-2-YL-6-(1,2,4,5-TETRAHYDRO-3-BENZAZEPIN-3-YL)PYRIMIDIN-4-YL]AMINO]PROPAN-1-OL
4ZN-1Ligand/IonZINC ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:1014 , GLU A:1016 , S2I A:2267 , HOH A:3001 , HOH A:3002BINDING SITE FOR RESIDUE FE2 A 1
02AC2SOFTWARECYS A:1199 , CYS A:1202 , CYS A:1226 , CYS A:1229BINDING SITE FOR RESIDUE ZN A4002
03AC3SOFTWAREHIS B:1014 , GLU B:1016 , S2I B:2267 , HOH B:3001 , HOH B:3002BINDING SITE FOR RESIDUE FE2 B 1
04AC4SOFTWARECYS B:1199 , CYS B:1202 , CYS B:1226 , CYS B:1229BINDING SITE FOR RESIDUE ZN B4002
05AC5SOFTWAREFE2 A:1 , ARG A:869 , THR A:954 , TYR A:1003 , LYS A:1005 , ARG A:1010 , THR A:1011 , PRO A:1012 , HIS A:1014 , GLU A:1016 , ASN A:1017 , ASN A:1024 , ASN A:1104 , HOH A:3002BINDING SITE FOR RESIDUE S2I A2267
06AC6SOFTWAREFE2 B:1 , ARG B:869 , SER B:893 , THR B:954 , ASN B:955 , TYR B:1003 , LYS B:1005 , ARG B:1010 , THR B:1011 , PRO B:1012 , HIS B:1014 , GLU B:1016 , ASN B:1017 , ASN B:1024 , ASN B:1104 , HOH B:3001 , HOH B:3002BINDING SITE FOR RESIDUE S2I B2267
07AC7SOFTWARETHR A:829 , ASN A:1089 , ALA A:1090 , THR A:1113 , CYS A:1115 , HOH A:3207BINDING SITE FOR RESIDUE EDO A2268
08AC8SOFTWAREPHE A:911 , GLY B:840 , ASP B:1084 , HOH B:3022 , HOH B:3186BINDING SITE FOR RESIDUE EDO B2268
09AC9SOFTWAREILE B:888 , TRP B:889 , ARG B:890 , HOH B:3331BINDING SITE FOR RESIDUE EDO B2269
10BC1SOFTWARESER A:853 , THR A:854 , GLN A:907 , GLY A:1028 , PRO A:1029 , ASN A:1103 , EDO A:2270 , HOH A:3037BINDING SITE FOR RESIDUE EDO A2269
11BC2SOFTWAREGLN A:907 , PHE A:911 , EDO A:2269 , HOH A:3088BINDING SITE FOR RESIDUE EDO A2270
12BC3SOFTWAREASN A:805 , ARG A:1077 , GLU B:920BINDING SITE FOR RESIDUE EDO A2271
13BC4SOFTWAREHIS A:1188 , HIS A:1197 , TYR A:1222BINDING SITE FOR RESIDUE EDO A2272
14BC5SOFTWAREGLY A:840 , ALA A:842 , GLY A:843 , PRO A:1082 , GLY A:1083 , ASP A:1084 , HOH A:3206BINDING SITE FOR RESIDUE EDO A2273
15BC6SOFTWARETYR A:812 , LEU A:813 , GLU A:814 , ARG A:839 , GLY A:840 , HOH A:3206 , PHE B:911 , GLN B:912BINDING SITE FOR RESIDUE EDO A2274
16BC7SOFTWARELEU A:971 , THR A:972 , ARG A:979 , VAL A:980 , VAL A:981 , HOH A:3127 , HOH A:3347BINDING SITE FOR RESIDUE EDO A2275
17BC8SOFTWAREILE A:888 , TRP A:889 , ARG A:890 , ASN A:1052 , HOH A:3204 , HOH A:3348BINDING SITE FOR RESIDUE EDO A2276

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5A1L)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:945 -Pro A:946
2Gly A:1028 -Pro A:1029
3Gly B:1028 -Pro B:1029

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A1L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A1L)

(-) Exons   (0, 0)

(no "Exon" information available for 5A1L)

(-) 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:443
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh....eee..hhhhhh.hhhhhhhhh....eeeeehhhhhhh.hhhhhhhhhhhhhh...eeeeeeee.....................eeeeeehhhhhhhhhhhhhhhhhhh.......eeeeeeeee......hhhhhhhhh..hhhhh.....hhhhhh..........eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhh...........hhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.........ee......ee..eeeeehhhhhh......hhhhhhhhh.....eeeee..hhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5a1l A  801 KDKLNPPTPSIYLENKRDAFFPPLHQFCTNPKNPVTVIRGLAGALKLDLGLFSTKTLVEANNEHMVEVRTQLLQPADENWDPTGTKKIWRCESNRSHTTIAKYAQYQASSFQESLREENEKGPFKTIKFGTNIDLSDNKKWKLQLHELTKLPAFARVVSAGNLLTHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFVVPEDYWGVLNDFCEKNNLNFLMSSWWPNLEDLYEANVPVYRFIQRPGDLVWINAGTVHWVQAVGWCNNIAWNVGPLTACQYKLAVERYEWNKLKSVKSPVPMVHLSWNMARNIKVSDPKLFEMIKYCLLKILKQYQTLREALVAAGKEVIWHGRTNDEPAHYCSICEVEVFNLLFVTNESNTQKTYIVHCHDCARKTSKSLENFVVLEQYKMEDLIQVYDQFTLALSLSS 1266
                                   810       820       830       840       850       860       870       880       890       900       910       920|      953       963       973       983       993      1003      1013      1023      1033      1043      1053      1063      1073      1083      1093      1103      1113      1123      1133      1143      1153      1163      1173      1183      1193      1203      1213      1223      1233      1243      1253      1263   
                                                                                                                                                 920|                                                                                                                                                                                                                                                                                                                                  
                                                                                                                                                  944                                                                                                                                                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:439
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee..hhhhhh.hhhhhhhhh....eeeeehhhhhhh.hhhhhhhhhhhhhhh..eeeeeeee.....................eeeeeehhhhhhhhhhhhhhhhhhhh...eeeeeeeee......hhhhhhhhh..hhhhh.....................eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhh............hhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.........ee......ee..eeeeehhhhhh......hhhhhhhhh.....eeeee..hhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5a1l B  802 DKLNPPTPSIYLENKRDAFFPPLHQFCTNPKNPVTVIRGLAGALKLDLGLFSTKTLVEANNEHMVEVRTQLLQPADENWDPTGTKKIWRCESNRSHTTIAKYAQYQASSFQESLREENEFKTIKFGTNIDLSDNKKWKLQLHELTKLPAFARVVSAGNLLTHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFVVPEDYWGVLNDFCEKNNLNFLMSSWWPNLEDLYEANVPVYRFIQRPGDLVWINAGTVHWVQAVGWCNNIAWNVGPLTACQYKLAVERYEWNKLKSVKSPVPMVHLSWNMARNIKVSDPKLFEMIKYCLLKILKQYQTLREALVAAGKEVIWHGRTNDEPAHYCSICEVEVFNLLFVTNESNTQKTYIVHCHDCARKTSKSLENFVVLEQYKMEDLIQVYDQFTLALSLSS 1266
                                   811       821       831       841       851       861       871       881       891       901       911       947       957       967       977       987       997      1007      1017      1027      1037      1047      1057      1067      1077      1087      1097      1107      1117      1127      1137      1147      1157      1167      1177      1187      1197      1207      1217      1227      1237      1247      1257         
                                                                                                                                                920|                                                                                                                                                                                                                                                                                                                               
                                                                                                                                                 947
   Legend:   → Mismatch (orange background)
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    → 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 5A1L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A1L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A1L)

(-) Gene Ontology  (10, 14)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        UTY_HUMAN | O14607: 3zli 3zpo 4uf0 5fxv 5fxw 5fxx 5fxz 5fy0 5fy1 5fy7 5fym

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