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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF LSD1-COREST IN COMPLEX WITH (-)-TRANS-2-PHENYLCYCLOPROPYL-1-AMINE

Authors :   C. Binda, S. Valente, M. Romanenghi, S. Pilotto, R. Cirilli, A. Karytinos, G. Ciossani, O. A. Botrugno, F. Forneris, M. Tardugno, D. E. Edmondson, S. Minucci, A. Mattevi, A. Mai

Date :   31 Mar 10 (Deposition) - 05 May 10 (Release) - 12 Oct 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.30

Chains :   Asym./Biol. Unit : A,B

Keywords :   Amine Oxidase, Chromatin Regulator, Histone Inhibitor Binding, Methylation, Nucleosome Core, Oxidoreductase, Oxidoreductase/Repressor Complex, Chromatin Remodelling, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Binda, S. Valente, M. Romanenghi, S. Pilotto, R. Cirilli, A. Karytinos, G. Ciossani, O. A. Botrugno, F. Forneris, M. Tardugno, D. E. Edmondson, S. Minucci, A. Mattevi, A. Mai
Biochemical, Structural, And Biological Evaluation Of Tranylcypromine Derivatives As Inhibitors Of Histone Demethylases Lsd1 And Lsd2.
J. Am. Chem. Soc. V. 132 6827 2010
PubMed-ID: 20415477 | Reference-DOI: 10.1021/JA101557K

Molecule 1 - LYSINE-SPECIFIC HISTONE DEMETHYLASE 1
	Chains	:	A
	EC Number	:	1.-.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	LYSINE-SPECIFIC HISTONE DEMETHYLASE LSD1, FLAVIN-CONTAINING AMINE OXIDASE DOMAIN-CONTAINING PROTEIN 2, BRAF35-HDAC COMPLEX PROTEIN BHC110

Molecule 2 - REST COREPRESSOR 1
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	COREPRESSOR COREST, PROTEIN COREST

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	TCA	1	Ligand/Ion	PHENYLETHYLENECARBOXYLIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:285 , GLY A:287 , VAL A:288 , SER A:289 , LEU A:307 , GLU A:308 , ALA A:309 , ARG A:310 , GLY A:314 , GLY A:315 , ARG A:316 , VAL A:317 , LEU A:329 , GLY A:330 , ALA A:331 , MET A:332 , VAL A:333 , THR A:588 , ALA A:589 , VAL A:590 , THR A:624 , LEU A:625 , PRO A:626 , TRP A:751 , TRP A:756 , SER A:760 , TYR A:761 , GLY A:800 , GLU A:801 , ALA A:809 , THR A:810 , VAL A:811 , TCA A:901	BINDING SITE FOR RESIDUE FAD A 900
2	AC2	SOFTWARE	MET A:332 , THR A:335 , LYS A:661 , TYR A:761 , FAD A:900	BINDING SITE FOR RESIDUE TCA A 901

(no "SS Bond" information available for 2XAJ)

Asymmetric/Biological Unit

No.	Residues
1	Ala A:240	-	Pro A:241
2	Pro A:470	-	Pro A:471
3	Gln A:633	-	Pro A:634
4	Val A:640	-	Pro A:641

Asymmetric/Biological Unit (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_076366	E	379	K	KDM1A_HUMAN	Disease (CPRF)	864309715	A	E	379	K
2	UniProt	VAR_076367	D	556	G	KDM1A_HUMAN	Disease (CPRF)	864309716	A	D	556	G
3	UniProt	VAR_076368	Y	761	H	KDM1A_HUMAN	Disease (CPRF)	864309714	A	Y	761	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SWIRM	PS50934	SWIRM domain profile.	KDM1A_HUMAN	174-273	1	A:174-273
2	SANT	PS51293	SANT domain profile.	RCOR1_HUMAN	190-241 381-432	1	- B:378-429

Asymmetric/Biological Unit (22, 22)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000262241	1	ENSE00001420913	chr14:103059233-103059524	292	RCOR1_HUMAN	1-98	98	0	-	-
1.2	ENST00000262241	2	ENSE00000660501	chr14:103059603-103059662	60	RCOR1_HUMAN	98-118	21	0	-	-
1.3	ENST00000262241	3	ENSE00000870514	chr14:103148232-103148315	84	RCOR1_HUMAN	118-146	29	0	-	-
1.4	ENST00000262241	4	ENSE00001678988	chr14:103167615-103167667	53	RCOR1_HUMAN	146-163	18	0	-	-
1.5	ENST00000262241	5	ENSE00001719953	chr14:103173688-103173849	162	RCOR1_HUMAN	164-217	54	0	-	-
1.6	ENST00000262241	6	ENSE00000660506	chr14:103174802-103174920	119	RCOR1_HUMAN	218-257	40	0	-	-
1.7	ENST00000262241	7	ENSE00000870515	chr14:103177272-103177350	79	RCOR1_HUMAN	257-283	27	0	-	-
1.8	ENST00000262241	8	ENSE00000660508	chr14:103180760-103180954	195	RCOR1_HUMAN	284-348	65	1	B:308-345	38
1.9	ENST00000262241	9	ENSE00000660509	chr14:103187344-103187421	78	RCOR1_HUMAN	349-374	26	1	B:346-371	26
1.10	ENST00000262241	10	ENSE00000660510	chr14:103187657-103187714	58	RCOR1_HUMAN	375-394	20	1	B:372-391	20
1.11	ENST00000262241	11	ENSE00000870516	chr14:103188524-103188753	230	RCOR1_HUMAN	394-470	77	1	B:391-440	50
1.12	ENST00000262241	12	ENSE00001152549	chr14:103192805-103196912	4108	RCOR1_HUMAN	471-482	12	0	-	-

2.1a	ENST00000356634	1a	ENSE00001422377	chr1:23345941-23346440	500	KDM1A_HUMAN	1-117	117	0	-	-
2.2	ENST00000356634	2	ENSE00000388542	chr1:23356962-23357127	166	KDM1A_HUMAN	118-173	56	1	A:171-173	3
2.4a	ENST00000356634	4a	ENSE00000759117	chr1:23376880-23377013	134	KDM1A_HUMAN	173-217	45	1	A:173-217	45
2.5	ENST00000356634	5	ENSE00000859702	chr1:23380254-23380332	79	KDM1A_HUMAN	218-244	27	1	A:218-244	27
2.6a	ENST00000356634	6a	ENSE00000859703	chr1:23381562-23381654	93	KDM1A_HUMAN	244-275	32	1	A:244-275	32
2.7	ENST00000356634	7	ENSE00000859704	chr1:23382425-23382531	107	KDM1A_HUMAN	275-310	36	1	A:275-310	36
2.8	ENST00000356634	8	ENSE00000859705	chr1:23383977-23384058	82	KDM1A_HUMAN	311-338	28	1	A:311-338	28
2.9	ENST00000356634	9	ENSE00000759111	chr1:23385566-23385660	95	KDM1A_HUMAN	338-369	32	1	A:338-369	32
2.11	ENST00000356634	11	ENSE00000759110	chr1:23395032-23395174	143	KDM1A_HUMAN	370-417	48	1	A:370-417	48
2.12	ENST00000356634	12	ENSE00000759108	chr1:23395554-23395644	91	KDM1A_HUMAN	417-447	31	1	A:417-447	31
2.13	ENST00000356634	13	ENSE00000859709	chr1:23397718-23397852	135	KDM1A_HUMAN	448-492	45	1	A:448-492	45
2.14	ENST00000356634	14	ENSE00000759106	chr1:23398617-23398690	74	KDM1A_HUMAN	493-517	25	1	A:493-517	25
2.15b	ENST00000356634	15b	ENSE00000388553	chr1:23399785-23399896	112	KDM1A_HUMAN	517-554	38	1	A:517-554	38
2.16a	ENST00000356634	16a	ENSE00000759050	chr1:23403721-23403853	133	KDM1A_HUMAN	555-599	45	1	A:555-599	45
2.17b	ENST00000356634	17b	ENSE00000859713	chr1:23405483-23405670	188	KDM1A_HUMAN	599-661	63	1	A:599-661	63
2.18b	ENST00000356634	18b	ENSE00000859714	chr1:23406046-23406160	115	KDM1A_HUMAN	662-700	39	1	A:662-700	39
2.19	ENST00000356634	19	ENSE00000859715	chr1:23407939-23408066	128	KDM1A_HUMAN	700-742	43	1	A:700-742	43
2.20	ENST00000356634	20	ENSE00000759046	chr1:23408713-23408859	147	KDM1A_HUMAN	743-791	49	1	A:743-791	49
2.21c	ENST00000356634	21c	ENSE00001564450	chr1:23409672-23410182	511	KDM1A_HUMAN	792-852	61	1	A:792-836	45

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:666
 aligned with KDM1A_HUMAN | O60341 from UniProtKB/Swiss-Prot  Length:852

    Alignment length:666
                                   180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830      
          KDM1A_HUMAN   171 PSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLGAMYTL 836
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2xajA01 A:171-279 'winged helix' repressor DNA binding domain                                                ------------------------------------------------------------------------------------------------------------------------------2xajA03 A:406-521  [code=1.10.287.80, no name defined]                                                              --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---SWIRM-2xajA02 A:174-264                                                                    -----------------------Amino_oxidase-2xajA01 A:288-826                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            ---------- Pfam domains
         Sec.struct. author ..hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh..hhhhhhhhhhhhhhhhhhh....................eeeee..hhhhhhhhhhhhhh..eeeee...........eeee..eeee....ee......hhhhhhhhh...eee...............hhhhhhhhhhhhhhhhhhhhhhhhh....ee..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh...........hhhhhhh.....eee....hhhhhhhhh..eee..eeeeeeeee..eeeeeeee......eeeeee.eeee..hhhhhhh.....eee...hhhhhhhhhhhee...eeeeee...........eee.............eeee.....eeeeeehhhhhhhhh..hhhhhhhhhhhhhhhhhh........eeee.............ee......hhhhhhhhh.................eee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------K--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------H--------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---SWIRM  PDB: A:174-273 UniProt: 174-273                                                              ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 2 (1) 2.2--------------------------------------------Exon 2.5  PDB: A:218-244   ------------------------------Exon 2.7  PDB: A:275-310            Exon 2.8  PDB: A:311-338    -------------------------------Exon 2.11  PDB: A:370-417 UniProt: 370-417      ------------------------------Exon 2.13  PDB: A:448-492 UniProt: 448-492   Exon 2.14  PDB: A:493-517-------------------------------------Exon 2.16a  PDB: A:555-599 UniProt: 555-599  --------------------------------------------------------------Exon 2.18b  PDB: A:662-700             ------------------------------------------Exon 2.20  PDB: A:743-791 UniProt: 743-791       Exon 2.21c  PDB: A:792-836 UniProt: 792-852   Transcript 2 (1)
           Transcript 2 (2) --Exon 2.4a  PDB: A:173-217 UniProt: 173-217   --------------------------Exon 2.6a  PDB: A:244-275       --------------------------------------------------------------Exon 2.9  PDB: A:338-369        -----------------------------------------------Exon 2.12  PDB: A:417-447      ---------------------------------------------------------------------Exon 2.15b  PDB: A:517-554            --------------------------------------------Exon 2.17b  PDB: A:599-661 UniProt: 599-661                    --------------------------------------Exon 2.19  PDB: A:700-742 UniProt: 700-742 ---------------------------------------------------------------------------------------------- Transcript 2 (2)
                 2xaj A 171 PSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLGAMYTL 836
                                   180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830

Chain B from PDB  Type:PROTEIN  Length:133
 aligned with RCOR1_HUMAN | Q9UKL0 from UniProtKB/Swiss-Prot  Length:485

    Alignment length:133
                                   320       330       340       350       360       370       380       390       400       410       420       430       440   
          RCOR1_HUMAN   311 RKPPKGMFLSQEDVEAVSANATAATTVLRQLDMELVSVKRQIQNIKQTNSALKEKLDGGIEPYRLPEVIQKCNARWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNYRRRFNIDEVLQEWEAE 443
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------Myb_DNA-binding-2xajB01 B:378-422            ------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh............hhhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhh....hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (1) ----------------------------------------------------------------------SANT  PDB: B:378-429 UniProt: 381-432               ----------- PROSITE (1)
           Transcript 1 (1) Exon 1.8  PDB: B:308-345 [INCOMPLETE] Exon 1.9  PDB: B:346-371  Exon 1.10           ------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------Exon 1.11  PDB: B:391-440 UniProt: 394-470         Transcript 1 (2)
                 2xaj B 308 RKPPKGMFLSQEDVEAVSANATAATTVLRQLDMELVSVKRQIQNIKQTNSALKEKLDGGIEPYRLPEVIQKCNARWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNYRRRFNIDEVLQEWEAE 440
                                   317       327       337       347       357       367       377       387       397       407       417       427       437

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 '\|'

(no "SCOP Domain" information available for 2XAJ)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Arc Repressor Mutant, subunit A (1030)

Homologous Superfamily: 'winged helix' repressor DNA binding domain (507)

Homo sapiens. Organism_taxid: 9606. (6)

2xajA01

A:171-279

Topology: Helix Hairpins (718)

Homologous Superfamily: [code=1.10.287.80, no name defined] (43)

Homo sapiens. Organism_taxid: 9606. (6)

2xajA03

A:406-521

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: Myb_DNA-binding (17)

Homo sapiens (Human) (17)

Myb_DNA-binding-2xajB01

B:378-422

Clan: NADP_Rossmann (1239)

Family: Amino_oxidase (60)

Homo sapiens (Human) (37)

Amino_oxidase-2xajA01

A:288-826

Clan: no clan defined [family: SWIRM] (13)

Family: SWIRM (13)

Homo sapiens (Human) (13)

SWIRM-2xajA02

A:174-264

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (KDM1A_HUMAN | O60341)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0043426	MRF binding	Interacting selectively and non-covalently with Myogenic Regulatory Factor (MRF), a member of the basic Helix-Loop-Helix (bHLH) superfamily of transcription factors.
	GO:0001085	RNA polymerase II transcription factor binding	Interacting selectively and non-covalently with an RNA polymerase II transcription factor, any protein required to initiate or regulate transcription by RNA polymerase II.
	GO:0050681	androgen receptor binding	Interacting selectively and non-covalently with an androgen receptor.
	GO:0003682	chromatin binding	Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
	GO:0032451	demethylase activity	Catalysis of the removal of a methyl group from a substrate.
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	GO:0050660	flavin adenine dinucleotide binding	Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
	GO:0004407	histone deacetylase activity	Catalysis of the reaction: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction represents the removal of an acetyl group from a histone, a class of proteins complexed to DNA in chromatin and chromosomes.
	GO:0032452	histone demethylase activity	Catalysis of the removal of a methyl group from a histone.
	GO:0032453	histone demethylase activity (H3-K4 specific)	Catalysis of the removal of a methyl group from lysine at position 4 of the histone H3 protein.
	GO:0032454	histone demethylase activity (H3-K9 specific)	Catalysis of the reaction: histone H3 N6-methyl-L-lysine (position 9) + alpha-ketoglutarate + O2 = succinate + CO2 + formaldehyde + lysine. This reaction is the removal of a methyl group from lysine at position 9 of the histone H3 protein.
	GO:0034648	histone demethylase activity (H3-dimethyl-K4 specific)	Catalysis of the removal of a methyl group from dimethylated lysine at position 4 of the histone H3 protein.
	GO:0030374	ligand-dependent nuclear receptor transcription coactivator activity	The function of a transcription cofactor that activates transcription in conjuction with a ligand-dependent nuclear receptor from a RNA polymerase II promoter; does not bind DNA itself.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0002039	p53 binding	Interacting selectively and non-covalently with one of the p53 family of proteins.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0042162	telomeric DNA binding	Interacting selectively and non-covalently with a telomere, a specific structure at the end of a linear chromosome required for the integrity and maintenance of the end.
	GO:0061752	telomeric repeat-containing RNA binding	Interacting selectively and non-covalently with long non-coding RNA molecules transcribed from subtelomeric regions in most eukaryotes. Telomeric repeat-containing RNA (TERRA) molecules consist of subtelomeric-derived sequences and G-rich telomeric repeats.
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	GO:0008134	transcription factor binding	Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
	GO:0044212	transcription regulatory region DNA binding	Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
biological process
	GO:0007596	blood coagulation	The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
	GO:0008283	cell proliferation	The multiplication or reproduction of cells, resulting in the expansion of a cell population.
	GO:0034644	cellular response to UV	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers.
	GO:0071480	cellular response to gamma radiation	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a gamma radiation stimulus. Gamma radiation is a form of electromagnetic radiation (EMR) or light emission of a specific frequency produced from sub-atomic particle interaction, such as electron-positron annihilation and radioactive decay. Gamma rays are generally characterized as EMR having the highest frequency and energy, and also the shortest wavelength, within the electromagnetic radiation spectrum.
	GO:0030851	granulocyte differentiation	The process in which a myeloid precursor cell acquires the specialized features of a granulocyte. Granulocytes are a class of leukocytes characterized by the presence of granules in their cytoplasm. These cells are active in allergic immune reactions such as arthritic inflammation and rashes. This class includes basophils, eosinophils and neutrophils.
	GO:0034720	histone H3-K4 demethylation	The modification of histone H3 by the removal of a methyl group from lysine at position 4 of the histone.
	GO:0033169	histone H3-K9 demethylation	The modification of histone H3 by the removal of a methyl group from lysine at position 9 of the histone.
	GO:0016575	histone deacetylation	The modification of histones by removal of acetyl groups.
	GO:0001701	in utero embryonic development	The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0055001	muscle cell development	The process whose specific outcome is the progression of a muscle cell over time, from its formation to the mature structure. Muscle cell development does not include the steps involved in committing an unspecified cell to the muscle cell fate.
	GO:0043392	negative regulation of DNA binding	Any process that stops or reduces the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).
	GO:0043518	negative regulation of DNA damage response, signal transduction by p53 class mediator	Any process that stops, prevents, or reduces the frequency, rate or extent of the cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage.
	GO:0051572	negative regulation of histone H3-K4 methylation	Any process that stops, prevents, or reduces the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 4 of histone H3.
	GO:0051573	negative regulation of histone H3-K9 methylation	Any process that stops, prevents, or reduces the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 9 of histone H3.
	GO:1902166	negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator	Any process that stops, prevents or reduces the frequency, rate or extent of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator.
	GO:0032091	negative regulation of protein binding	Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding.
	GO:0043433	negative regulation of sequence-specific DNA binding transcription factor activity	Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
	GO:0000122	negative regulation of transcription from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0021983	pituitary gland development	The progression of the pituitary gland over time from its initial formation until its mature state. The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands.
	GO:0045648	positive regulation of erythrocyte differentiation	Any process that activates or increases the frequency, rate or extent of erythrocyte differentiation.
	GO:0033184	positive regulation of histone ubiquitination	Any process that activates or increases the frequency, rate or extent of the addition of a ubiquitin group to a histone protein.
	GO:0046886	positive regulation of hormone biosynthetic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of hormones.
	GO:0045654	positive regulation of megakaryocyte differentiation	Any process that activates or increases the frequency, rate or extent of megakaryocyte differentiation.
	GO:2000179	positive regulation of neural precursor cell proliferation	Any process that activates or increases the frequency, rate or extent of neural precursor cell proliferation.
	GO:0051091	positive regulation of sequence-specific DNA binding transcription factor activity	Any process that activates or increases the frequency, rate or extent of activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
	GO:2000648	positive regulation of stem cell proliferation	Any process that activates or increases the frequency, rate or extent of stem cell proliferation.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0006482	protein demethylation	The removal of a methyl group, from a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom.
	GO:1903827	regulation of cellular protein localization	Any process that modulates the frequency, rate or extent of cellular protein localization. Cellular protein localization is any process in which a protein is transported to, and/or maintained in, a specific location and encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell.
	GO:0010569	regulation of double-strand break repair via homologous recombination	Any process that modulates the frequency, rate or extent of the error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences.
	GO:0010725	regulation of primitive erythrocyte differentiation	Any process that modulates the rate, frequency, or extent of primitive erythrocyte differentiation. Primitive erythrocyte differentiation occurs as part of the process of primitive hemopoiesis.
	GO:0006357	regulation of transcription from RNA polymerase II promoter	Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:1990391	DNA repair complex	A protein complex involved in DNA repair processes including direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
	GO:0000790	nuclear chromatin	The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
	GO:0000784	nuclear chromosome, telomeric region	The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
	GO:0005667	transcription factor complex	A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

Chain B (RCOR1_HUMAN | Q9UKL0)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0004407	histone deacetylase activity	Catalysis of the reaction: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction represents the removal of an acetyl group from a histone, a class of proteins complexed to DNA in chromatin and chromosomes.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0003714	transcription corepressor activity	Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
	GO:0008134	transcription factor binding	Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
	GO:0044212	transcription regulatory region DNA binding	Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
	GO:0001078	transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter.
biological process
	GO:0007596	blood coagulation	The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
	GO:0070933	histone H4 deacetylation	The modification of histone H4 by the removal of one or more acetyl groups.
	GO:0000122	negative regulation of transcription from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:1990391	DNA repair complex	A protein complex involved in DNA repair processes including direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0005667	transcription factor complex	A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.
	GO:0017053	transcriptional repressor complex	A protein complex that possesses activity that prevents or downregulates transcription.

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		Pro A:470 - Pro A:471	[ RasMol ]
		Val A:640 - Pro A:641	[ RasMol ]

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2com	THE SOLUTION STRUCTURE OF THE 33RD FIBRONECTIN TYPE IIIDOMAIN OF HUMAN TENASCIN-X
2h94	CRYSTAL STRUCTURE AND MECHANISM OF HUMAN LYSINE-SPECIFICDEMETHYLASE-1
2iw5	STRUCTURAL BASIS FOR COREST-DEPENDENT DEMETHYLATION OF NUCLEOSOMES BY THE HUMAN LSD1 HISTONE DEMETHYLASE
2uxn	STRUCTURAL BASIS OF HISTONE DEMETHYLATION BY LSD1 REVEALED BY SUICIDE INACTIVATION
2uxx	HUMAN LSD1 HISTONE DEMETHYLASE-COREST IN COMPLEX WITH AN FAD-TRANYLCYPROMINE ADDUCT
2v1d	STRUCTURAL BASIS OF LSD1-COREST SELECTIVITY IN HISTONE H3 RECOGNITION
2x0l	CRYSTAL STRUCTURE OF A NEURO-SPECIFIC SPLICING VARIANT OF HUMAN HISTONE LYSINE DEMETHYLASE LSD1.
2xaf	CRYSTAL STRUCTURE OF LSD1-COREST IN COMPLEX WITH PARA-BROMO-CIS-2-PHENYLCYCLOPROPYL-1 -AMINE
2xag	CRYSTAL STRUCTURE OF LSD1-COREST IN COMPLEX WITH PARA-BROMO-(-)-TRANS-2- PHENYLCYCLOPROPYL-1-AMINE
2xah	CRYSTAL STRUCTURE OF LSD1-COREST IN COMPLEX WITH (PLUS)-TRANS-2-PHENYLCYCLOPROPYL-1- AMINE
2xaq	CRYSTAL STRUCTURE OF LSD1-COREST IN COMPLEX WITH A TRANYCYPROMINE DERIVATIVE (MC2584, 13B)
2xas	CRYSTAL STRUCTURE OF LSD1-COREST IN COMPLEX WITH A TRANYCYPROMINE DERIVATIVE (MC2580, 14E)

Description

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Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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SAPs(SNPs)/Variants (3, 3)

PROSITE Motifs (2, 2)

Exons (22, 22)

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CATH Domains (2, 2)

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Gene Ontology (71, 85)

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