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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN JMJD2D/KDM4D APOENZYME
 
Authors :  S. Krishnan, R. C. Trievel
Date :  22 Oct 12  (Deposition) - 21 Nov 12  (Release) - 30 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Jumonji C Demethylase, Jmjd2/Kdm4 Family, Beta Barrel Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Krishnan, R. C. Trievel
Structural And Functional Analysis Of Jmjd2D Reveals Molecular Basis For Site-Specific Demethylation Among Jmjd2 Demethylases.
Structure V. 21 98 2013
PubMed-ID: 23219879  |  Reference-DOI: 10.1016/J.STR.2012.10.018

(-) Compounds

Molecule 1 - LYSINE-SPECIFIC DEMETHYLASE 4D
    Chains: A, B
    EC Number: 1.14.11.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHT4
    Expression System Strain: BL21(ROSETTA 2)
    Expression System Taxid: 469008
    Expression System Vector Type: PLAMSID
    Fragment: UNP RESIDUES 12-341
    Gene: JHDM3D, JMJD2D, KDM4D
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3D, JUMONJI DOMAIN-CONTAINING PROTEIN 2D

 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  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2NI2Ligand/IonNICKEL (II) ION
3ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2NI-1Ligand/IonNICKEL (II) ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2NI-1Ligand/IonNICKEL (II) ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:192 , GLU A:194 , HIS A:280 , HOH A:507 , HOH A:526BINDING SITE FOR RESIDUE NI A 401
2AC2SOFTWARECYS A:238 , HIS A:244 , CYS A:310 , CYS A:312BINDING SITE FOR RESIDUE ZN A 402
3AC3SOFTWAREASN A:15 , ASN A:17 , PHE A:261 , ASN A:262BINDING SITE FOR RESIDUE ACT A 403
4AC4SOFTWAREGLU A:27 , HOH A:528BINDING SITE FOR RESIDUE ACT A 404
5AC5SOFTWAREHIS B:192 , GLU B:194 , HIS B:280 , HOH B:502BINDING SITE FOR RESIDUE NI B 401
6AC6SOFTWARECYS B:238 , HIS B:244 , CYS B:310 , CYS B:312BINDING SITE FOR RESIDUE ZN B 402

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1B:238 -B:310

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4HOO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HOO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HOO)

(-) Exons   (0, 0)

(no "Exon" information available for 4HOO)

(-) 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:327
                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains d4hooa_ A: JMJD2D core                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee........hhhhhhhhhhhhhhhhh.eeee..................ee...eeeeeeee..eeeeeeee...eehhhhhhhh...........hhhhhhhhhhhh......eeeeeee.................hhhhhhhhhhh.........eeeee....eeeee.hhhhheeeeeeeee..eeeee.hhhhhhhhhhhhhhhh.....hhhhhh.eeehhhhhhhh....eeeee....eeee.....eeeee...eeeeeeee.hhhhhhhhh...............hhhhhhhhh..hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hoo A  12 QNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARETYDNISEILIATPLQQVASGRAGVFTQYHKKAAAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQD 341
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231  ||   244       254       264       274       284       294       304       314       324       334       
                                                                                                                                                                                                                                                        234|                                                                                                       
                                                                                                                                                                                                                                                         238                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:330
                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d4hoob_ B: JMJD2D core                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eee...hhhhhhhhhhhhhhhhhhhhhh.eeee...........hhhhhh.ee...eeeeeeee..eeeeeeee...eehhhhhhhhh..........hhhhhhhhhhhhh.....eeeeeee.................hhhhhhhhhhh.........eeeee....eeeee.hhhhheeeeeeeee..eeeee.hhhhhhhhhhhhhhhh........hhhhhh.eeehhhhhhhh....eeeee....eeee.....eeeee...eeeeeeee.hhhhhhhhhhh.............hhhhhhhhh..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hoo B  12 QNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARETYDNISEILIATPLQQVASGRAGVFTQYHKKAAAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQD 341
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341
   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  (1, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HOO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HOO)

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)

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  4hoo
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  KDM4D_HUMAN | Q6B0I6
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  1.14.11.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        KDM4D_HUMAN | Q6B0I6: 3dxt 3dxu 4d6q 4d6r 4d6s 4hon 5f5a 5f5c 5fp4 5fp7 5fp8 5fp9 5fpa 5fpb 5ph0 5ph1 5ph2 5ph3 5ph4 5ph5 5ph6 5ph7 5ph8 5ph9 5pha 5phb 5phc 5phd 5phe 5phf 5phg 5phh 5phi 5phj 5phk 5phl 5phm 5phn 5pho 5php 5phq 5phr 5phs 5pht 5phu 5phv 5phw 5phx 5phy 5phz 5pi0 5pi1 5pi2 5pi3 5pi4 5pi5 5pi6 5pi7 5pi8 5pi9 5pia 5pib 5pic 5pid 5pie 5pif 5pig 5pih 5pii 5pij 5pik 5pil 5pim 5pin 5pio 5pip 5piq 5pir 5pis 5pit 5piu 5piv 5piw 5pix 5piy 5piz 5pj0 5pj1 5pj2 5pj3 5pj4 5pj5 5pj6 5pj7 5pj8 5pj9 5pja 5pjb 5pjc 5pjd 5pje 5pjf 5pjg 5pjh 5pji 5pjj 5pjk 5pjl 5pjm 5pjn 5pjo 5pjp 5pjq 5pjr 5pjs 5pjt 5pju 5pjv 5pjw 5pjx 5pjy 5pjz 5pk0 5pk1 5pk2 5pk3 5pk4 5pk5 5pk6 5pk7 5pk8 5pk9 5pka 5pkb 5pkc 5pkd 5pke 5pkf 5pkg 5pkh 5pki 5pkj 5pkk 5pkl 5pkm 5pkn 5pko 5pkp 5pkq 5pkr 5pks 5pkt 5pku 5pkv 5pkw 5pkx 5pky 5pkz 5pl0 5pl1 5pl2 5pl3 5pl4 5pl5 5pl6 5pl7 5pl8 5pl9 5pla 5plb 5plc 5pld 5ple 5plf 5plg 5plh 5pli 5plj 5plk 5pll 5plm 5pln 5plo 5plp 5plq 5plr 5pls 5plt 5plu 5plv 5plw 5plx 5ply 5plz 5pm0 5pm1 5pm2 5pm3 5pm4 5pm5 5pm6 5pm7 5pm8 5pm9 5pma 5pmb 5pmc 5pmd 5pme 5pmf 5pmg 5pmh 5pmi 5pmj 5pmk 5pml 5pmm 5pmn 5pmo 5pmp 5pmq 5pmr 5pms 5pmt 5pmu 5pmv 5pmw 5pmx 5pmy 5pmz 5pn0 5pn1 5pn2 5pn3 5pn4 5pn5 5pn6 5pn7 5pn8 5pn9 5pna 5pnb 5pnc 5pnd 5pne 5pnf 5png 5pnh 5pni 5pnj 5pnk 5pnl 5pnm 5pnn 5pno 5pnp 5pnq 5pnr 5pns 5pnu 5pnv 5pnw

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4HOO)