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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH PYRUVATE
 
Authors :  R. Nowak, J. Kopec, C. Johansson, A. Szykowska, F. Von Delft, C. H. Arro C. Bountra, A. Edwards, U. Oppermann
Date :  07 Mar 16  (Deposition) - 16 Mar 16  (Release) - 16 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Oxidoreductase, Jmjd2A, Kdm4A, Tca Intermediate (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Nowak, J. Kopec, C. Johansson, A. Szykowska, F. Von Delft, C. H. Arrowsmith, C. Bountra, A. Edwards, U. Oppermann
Crystal Structure Of Human Jmjd2A In Complex With Pyruvate
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - LYSINE-SPECIFIC DEMETHYLASE 4A
    ChainsA, B
    EC Number1.14.11.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentRESIDUES 4-354
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymJMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3A, JU MONJI DOMAIN-CONTAINING PROTEIN 2A

 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  (6, 28)

Asymmetric Unit (6, 28)
No.NameCountTypeFull Name
11KA1Ligand/Ion(2-HYDROXYETHOXY)ACETALDEHYDE
2DMS2Ligand/IonDIMETHYL SULFOXIDE
3EDO17Ligand/Ion1,2-ETHANEDIOL
4NI2Ligand/IonNICKEL (II) ION
5PYR4Ligand/IonPYRUVIC ACID
6ZN2Ligand/IonZINC ION
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
11KA-1Ligand/Ion(2-HYDROXYETHOXY)ACETALDEHYDE
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3EDO9Ligand/Ion1,2-ETHANEDIOL
4NI-1Ligand/IonNICKEL (II) ION
5PYR2Ligand/IonPYRUVIC ACID
6ZN-1Ligand/IonZINC ION
Biological Unit 2 (4, 12)
No.NameCountTypeFull Name
11KA1Ligand/Ion(2-HYDROXYETHOXY)ACETALDEHYDE
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3EDO8Ligand/Ion1,2-ETHANEDIOL
4NI-1Ligand/IonNICKEL (II) ION
5PYR2Ligand/IonPYRUVIC ACID
6ZN-1Ligand/IonZINC ION

(-) Sites  (27, 27)

Asymmetric Unit (27, 27)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:188 , GLU A:190 , HIS A:276 , PYR A:1355 , HOH A:2083BINDING SITE FOR RESIDUE NI A 501
02AC2SOFTWAREHIS B:188 , GLU B:190 , HIS B:276 , PYR B:1354 , HOH B:2090BINDING SITE FOR RESIDUE NI B 501
03AC3SOFTWARECYS B:234 , HIS B:240 , CYS B:306 , CYS B:308BINDING SITE FOR RESIDUE ZN B 502
04AC4SOFTWAREPHE A:185 , HIS A:188 , GLU A:190 , SER A:196 , ASN A:198 , TRP A:208 , HIS A:276 , NI A:501 , PYR A:1356BINDING SITE FOR RESIDUE PYR A1355
05AC5SOFTWAREPHE B:185 , HIS B:188 , GLU B:190 , SER B:196 , ASN B:198 , TRP B:208 , HIS B:276 , NI B:501 , PYR B:1355BINDING SITE FOR RESIDUE PYR B1354
06AC6SOFTWARETYR B:132 , TYR B:177 , PHE B:185 , ASN B:198 , LYS B:206 , SER B:288 , PYR B:1354 , EDO B:1364BINDING SITE FOR RESIDUE PYR B1355
07AC7SOFTWARETYR A:132 , TYR A:177 , ASN A:198 , LYS A:206 , SER A:288 , PYR A:1355 , EDO A:1365BINDING SITE FOR RESIDUE PYR A1356
08AC8SOFTWARECYS A:234 , HIS A:240 , CYS A:306 , CYS A:308BINDING SITE FOR RESIDUE ZN A3000
09AC9SOFTWAREPHE A:227 , PRO A:228 , GLY A:229 , SER A:230 , LYS B:105BINDING SITE FOR RESIDUE DMS A1357
10BC1SOFTWAREPHE B:227 , PRO B:228 , GLY B:229 , SER B:230BINDING SITE FOR RESIDUE DMS B1356
11BC2SOFTWAREHIS A:188 , THR A:189 , LEU A:238 , ARG A:239 , TYR A:275 , HOH A:2105BINDING SITE FOR RESIDUE EDO A1358
12BC3SOFTWARETYR B:121 , TRP B:122 , PHE B:185 , TRP B:187 , LEU B:244 , ILE B:245 , ALA B:277 , GLY B:278BINDING SITE FOR RESIDUE EDO B1357
13BC4SOFTWAREGLY B:80 , SER B:246 , LEU B:248 , HOH B:2067BINDING SITE FOR RESIDUE EDO B1358
14BC5SOFTWAREGLU B:235 , ALA B:236 , PHE B:237 , LEU B:238 , HOH B:2112 , HOH B:2132BINDING SITE FOR RESIDUE EDO B1359
15BC6SOFTWAREHOH A:2062 , THR B:76 , LEU B:81 , PHE B:82 , THR B:83 , PHE B:227BINDING SITE FOR RESIDUE EDO B1360
16BC7SOFTWAREGLY A:80 , PHE A:82 , TRP A:122 , SER A:246 , HOH A:2034BINDING SITE FOR RESIDUE EDO A1359
17BC8SOFTWAREGLU A:163 , LYS B:330 , HOH B:2152BINDING SITE FOR RESIDUE EDO A1360
18BC9SOFTWARETHR A:83 , PHE A:227 , SER A:230 , PHE A:237 , THR A:243 , HOH A:2116BINDING SITE FOR RESIDUE EDO A1361
19CC1SOFTWAREARG B:98 , ASN B:102BINDING SITE FOR RESIDUE EDO B1361
20CC2SOFTWARETYR B:106 , ASN B:128 , PRO B:130 , TRP B:181 , LYS B:182BINDING SITE FOR RESIDUE EDO B1362
21CC3SOFTWARETYR B:18 , LYS B:46 , GLU B:263 , GLU B:266 , HOH B:2006BINDING SITE FOR RESIDUE EDO B1363
22CC4SOFTWAREPHE A:114 , THR A:261 , GLU A:263 , HIS A:281BINDING SITE FOR RESIDUE EDO A1362
23CC5SOFTWAREASP A:158 , GLU A:161 , LYS A:162 , HOH A:2075BINDING SITE FOR RESIDUE EDO A1363
24CC6SOFTWAREGLU A:214 , HIS A:215BINDING SITE FOR RESIDUE EDO A1364
25CC7SOFTWAREPHE B:185 , HIS B:188 , LYS B:241 , PYR B:1355BINDING SITE FOR RESIDUE EDO B1364
26CC8SOFTWARETYR A:132 , PHE A:185 , PYR A:1356BINDING SITE FOR RESIDUE EDO A1365
27CC9SOFTWAREALA B:12 , GLU B:214 , HIS B:215 , PRO B:256 , HOH B:2122BINDING SITE FOR RESIDUE 1KA B1365

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FYI)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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   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:351
                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee..hhhhhhhhhhhhhhhhhhhhhhh.eeee.............hhhh.ee...eeeeeeee..eeeeeeee...eehhhhhhhhhh.........hhhhhhhhhhhhh.....eeeeeee.................hhhhhhhhhhh.........eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeehhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhh.............hhhhhhhhh..hhhhhhh............hhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fyi A   4 ESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFL 354
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353 

Chain B from PDB  Type:PROTEIN  Length:344
                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..hhhhhhhhhhhhhhhhhhhhhhh.eeee..................ee...eeeeeeee..eeeeeeee...eehhhhhhhhhh.........hhhhhhhhhhhhh.....eeeeeee.................hhhhhhhhh...........eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeehhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhh.............hhhhhhhhhhhhhhhhhh............hhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fyi B  10 PSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEF 353
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349    

   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 5FYI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (25, 25)

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 Related Entries

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

UniProtKB/Swiss-Prot
        KDM4A_HUMAN | O751642gf7 2gfa 2gp3 2gp5 2oq6 2oq7 2os2 2ot7 2ox0 2p5b 2pxj 2q8c 2q8d 2q8e 2qqr 2qqs 2vd7 2wwj 2ybk 2ybp 2ybs 3njy 3pdq 3rvh 3u4s 4ai9 4bis 4gd4 4ura 4v2v 4v2w 5a7n 5a7o 5a7p 5a7q 5a7s 5a7w 5a80 5anq 5d6w 5d6x 5d6y 5f2s 5f2w 5f32 5f37 5f39 5f3c 5f3e 5f3g 5f3i 5f5i 5fpv 5fwe 5fy8 5fyc 5fyh 5ly1 5ly2 5tvr 5tvs

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