5PHD - JenaLib

Title :   PANDDA ANALYSIS GROUP DEPOSITION -- CRYSTAL STRUCTURE OF JMJD2D IN COMPLEX WITH N09419A

Authors :   N. M. Pearce, T. Krojer, R. Talon, A. R. Bradley, M. Fairhead, R. Sethi, N E. Maclean, P. Collins, J. Brandao-Neto, A. Douangamath, Z. Renjie, A M. Vollmar, J. Ng, A. Szykowska, N. Burgess-Brown, P. E. Brennan, O. Co U. Oppermann, C. Bountra, C. H. Arrowsmith, A. Edwards, F. Von Delft

Date :   07 Feb 17 (Deposition) - 15 Mar 17 (Release) - 15 Mar 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.36

Chains :   Asym./Biol. Unit : A

Keywords :   Pandda, Sgc - Diamond I04-1 Fragment Screening, Jmj Domain, Epigenetics, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. M. Pearce, T. Krojer, A. R. Bradley, P. Collins, R. Nowak, R. Talon, B. Marsden, S. Kelm, J. Shi, D. Deane, F. Von Delft
Pandda Analysis Group Deposition
To Be Published
PubMed: search

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 18)

Sites (18, 18)

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:238 , HIS A:244 , CYS A:310 , CYS A:312	binding site for residue ZN A 401
02	AC2	SOFTWARE	HIS A:192 , GLU A:194 , HIS A:280 , OGA A:403 , HOH A:623	binding site for residue NI A 402
03	AC3	SOFTWARE	TYR A:136 , PHE A:189 , HIS A:192 , GLU A:194 , SER A:200 , ASN A:202 , LYS A:210 , TRP A:212 , HIS A:280 , NI A:402 , EDO A:411 , HOH A:623 , HOH A:703	binding site for residue OGA A 403
04	AC4	SOFTWARE	LYS A:150 , GLN A:151 , TRP A:152 , ASN A:153 , HIS A:156 , HOH A:536 , HOH A:660	binding site for residue EDO A 404
05	AC5	SOFTWARE	THR A:252 , ARG A:263 , HOH A:789	binding site for residue EDO A 405
06	AC6	SOFTWARE	GLU A:224 , ALA A:240 , PHE A:241 , LEU A:242 , TYR A:279 , SER A:308 , HOH A:507	binding site for residue EDO A 406
07	AC7	SOFTWARE	ASP A:64 , ASN A:65 , ILE A:66 , SER A:67 , GLU A:68 , ARG A:82 , 4NC A:418 , HOH A:525	binding site for residue EDO A 407
08	AC8	SOFTWARE	PHE A:118 , ARG A:263 , ILE A:264 , THR A:265 , HOH A:529	binding site for residue EDO A 408
09	AC9	SOFTWARE	TRP A:57 , LYS A:58 , ALA A:59 , ARG A:60 , TYR A:63 , TYR A:203 , HOH A:505 , HOH A:508 , HOH A:564 , HOH A:686	binding site for residue EDO A 409
10	AD1	SOFTWARE	SER A:80 , THR A:87 , CYS A:168 , LYS A:305 , 4NC A:415 , HOH A:524 , HOH A:615	binding site for residue EDO A 410
11	AD2	SOFTWARE	TYR A:181 , SER A:200 , ALA A:292 , ASN A:294 , OGA A:403	binding site for residue EDO A 411
12	AD3	SOFTWARE	ARG A:102 , HIS A:103 , ASN A:106 , HOH A:511 , HOH A:533 , HOH A:573	binding site for residue SO4 A 412
13	AD4	SOFTWARE	ARG A:123 , LYS A:124 , LYS A:127 , ASN A:128	binding site for residue SO4 A 413
14	AD5	SOFTWARE	PRO A:113 , LYS A:124 , ASN A:128 , TRP A:185 , LYS A:186 , HOH A:631	binding site for residue SO4 A 414
15	AD6	SOFTWARE	SER A:80 , VAL A:85 , THR A:87 , GLU A:167 , CYS A:168 , LEU A:230 , PHE A:231 , ILE A:301 , LYS A:305 , EDO A:410 , HOH A:524 , HOH A:615 , HOH A:654 , HOH A:723	binding site for residue 4NC A 415
16	AD7	SOFTWARE	LYS A:25 , ASN A:29 , GLU A:56 , TRP A:57 , GLN A:151 , HOH A:814 , HOH A:830 , HOH A:838 , HOH A:886 , HOH A:910	binding site for residue 4NC A 416
17	AD8	SOFTWARE	VAL A:78 , TYR A:89 , LYS A:91 , LYS A:305 , MET A:306 , GLN A:329 , GLU A:331 , ARG A:332 , HOH A:510 , HOH A:512 , HOH A:695 , HOH A:819 , HOH A:839 , HOH A:848	binding site for residue 4NC A 417
18	AD9	SOFTWARE	ARG A:82 , LEU A:230 , VAL A:253 , GLU A:256 , ASN A:257 , EDO A:407 , HOH A:534 , HOH A:651 , HOH A:741 , HOH A:785	binding site for residue 4NC A 418

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological 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:328
                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee........hhhhhhhhhhhhhhhhh.eeee..................ee...eeeeeeee..eeeeeeee...eehhhhhhhhh..........hhhhhhhhhhhhhhhh..eeeeeee.................hhhhhhhhhhh.........eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeehhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhh............hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5phd A  11 AQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKR 338
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330

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)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (18, 18)

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		4NC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NI	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		OGA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		AD1	[ RasMol ]	+environment [ RasMol ]
		AD2	[ RasMol ]	+environment [ RasMol ]
		AD3	[ RasMol ]	+environment [ RasMol ]
		AD4	[ RasMol ]	+environment [ RasMol ]
		AD5	[ RasMol ]	+environment [ RasMol ]
		AD6	[ RasMol ]	+environment [ RasMol ]
		AD7	[ RasMol ]	+environment [ RasMol ]
		AD8	[ RasMol ]	+environment [ RasMol ]
		AD9	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5phd)

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	5phd
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	KDM4D_HUMAN \| Q6B0I6
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description