PDB ID 2XAF     CHAIN A
Protein name LYSINE-SPECIFIC HISTONE DEMETHYLASE 1
Uniprot Accession O60341
The number of similar proteins 41
The number of binding states 4
The number of binding partners 4

Coloring

Unicolor (beige)

The number of binding partners

Group

Binding
state		 Binding partners
2XAF (CHAIN: A)
1 Q9UKL0  
2 Q9UKL0  
3 Q9UKL0   Q01101  
4 Q9UKL0   A0A310TTQ1  

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Only interaction residues
#binding
partners
  4
  3
  2
  1
  0

Sequence information

1   MLSGKKAAAA   AAAAAAAATG   TEAGPGTAGG   SENGSEVAAQ   PAGLSGPAEV   50
51   GPGAVGERTP   RKKEPPRASP   PGGLAEPPGS   AGPQAGPTVV   PGSATPMETG   100
101   IAETPEGRRT   SRRKRAKVEY   REMDESLANL   SEDEYYSEEE   RNAKAEKEKK   150
151   LPPPPPQAPP   EEENESEPEE   PSGVEGAAFQ   SRLPHDRMTS   QEAACFPDII   200
201   SGPQQTQKVF   LFIRNRTLQL   WLDNPKIQLT   FEATLQQLEA   PYNSDTVLVH   250
251   RVHSYLERHG   LINFGIYKRI   KPLPTKKTGK   VIIIGSGVSG   LAAARQLQSF   300
301   GMDVTLLEAR   DRVGGRVATF   RKGNYVADLG   AMVVTGLGGN   PMAVVSKQVN   350
351   MELAKIKQKC   PLYEANGQAV   PKEKDEMVEQ   EFNRLLEATS   YLSHQLDFNV   400
401   LNNKPVSLGQ   ALEVVIQLQE   KHVKDEQIEH   WKKIVKTQEE   LKELLNKMVN   450
451   LKEKIKELHQ   QYKEASEVKP   PRDITAEFLV   KSKHRDLTAL   CKEYDELAET   500
501   QGKLEEKLQE   LEANPPSDVY   LSSRDRQILD   WHFANLEFAN   ATPLSTLSLK   550
551   HWDQDDDFEF   TGSHLTVRNG   YSCVPVALAE   GLDIKLNTAV   RQVRYTASGC   600
601   EVIAVNTRST   SQTFIYKCDA   VLCTLPLGVL   KQQPPAVQFV   PPLPEWKTSA   650
651   VQRMGFGNLN   KVVLCFDRVF   WDPSVNLFGH   VGSTTASRGE   LFLFWNLYKA   700
701   PILLALVAGE   AAGIMENISD   DVIVGRCLAI   LKGIFGSSAV   PQPKETVVSR   750
751   WRADPWARGS   YSYVAAGSSG   NDYDLMAQPI   TPGPSIPGAP   QPIPRLFFAG   800
801   EHTIRNYPAT   VHGALLSGLR   EAGRIADQFL   GAMYTLPRQA   TPGVPAQQSP   850
851   SM           900

Variants

Residue AA Source dbSNP Clinical
Significance
 Allele
Frequency
(> 0.0001)		 Disease name
177_ALA SER 8.3kJPN
chr1:23376891 		rs765222197
- 0.0001 -
254_SER GLY 8.3kJPN
chr1:23381591 		rs532200849
- 0.0003 -
315_GLY TER ClinVar
chr1:23383989 		rs1553129293
Likely pathogenic - not provided [MedGen:CN517202]
332_MET VAL 8.3kJPN
chr1:23384040 		-
- 0.0001 -
344_VAL LEU 8.3kJPN
chr1:23385583 		-
- 0.0001 -
375_ASP GLY ClinVar
chr1:23395048 		rs1553130904
Likely pathogenic - not provided|Intellectual disability [MedGen:CN517202|Human Phenotype Ontology:HP:0000730,Human Phenotype Ontology:HP:0001249,Human Phenotype Ontology:HP:0001267,Human Phenotype Ontology:HP:0001286,Human Phenotype Ontology:HP:0002122,Human Phenotype Ontology:HP:0002192,Human Phenotype Ontology:HP:0002316,Human Phenotype Ontology:HP:0002382,Human Phenotype Ontology:HP:0002386,Human Phenotype Ontology:HP:0002402,Human Phenotype Ontology:HP:0002458,Human Phenotype Ontology:HP:0002482,Human Phenotype Ontology:HP:0002499,Human Phenotype Ontology:HP:0002543,Human Phenotype Ontology:HP:0003767,Human Phenotype Ontology:HP:0006833,Human Phenotype Ontology:HP:0007154,Human Phenotype Ontology:HP:0007176,Human Phenotype Ontology:HP:0007180,MONDO:MONDO:0001071,MeSH:D008607,MedGen:C3714756]
377_MET LEU 8.3kJPN
chr1:23395053 		-
- 0.0001 -
379_GLU LYS VAR_076366 rs864309715
LP/P - Cleft palate, psychomotor retardation, and distinctive facial features (CPRF) [MIM:616728]
379_GLU LYS ClinVar
chr1:23395059 		rs864309715
Pathogenic - Palatal anomalies-widely spaced teeth-facial dysmorphism-developmental delay syndrome [MONDO:MONDO:0014751,MedGen:C4225229,OMIM:616728,Orphanet:477993]
379_GLU ALA ClinVar
chr1:23395060 		rs2124508402
Likely pathogenic - not provided [MedGen:C3661900]
451_LEU TRP 8.3kJPN
chr1:23397728 		rs769906942
- 0.0002 -
471_PRO SER 8.3kJPN
chr1:23397787 		-
- 0.0001 -
489_ALA THR 8.3kJPN
chr1:23397841 		rs758354898
- 0.0001 -
520_TYR CYS 8.3kJPN
chr1:23399793 		-
- 0.0001 -
554_GLN ARG ClinVar
chr1:23399895 		rs2124523419
Likely pathogenic - Neurodevelopmental delay [Human Phenotype Ontology:HP:0012758,MedGen:C4022738]
555_ASP GLY ClinVar
chr1:23403722 		rs2124538211
Likely pathogenic - not provided [MedGen:C3661900]
555_ASP VAL ClinVar
chr1:23403722 		rs2124538211
Likely pathogenic - not provided [MedGen:C3661900]
556_ASP GLY VAR_076367 rs864309716
LP/P - Cleft palate, psychomotor retardation, and distinctive facial features (CPRF) [MIM:616728]
556_ASP GLY ClinVar
chr1:23403725 		rs864309716
Pathogenic - Palatal anomalies-widely spaced teeth-facial dysmorphism-developmental delay syndrome [MONDO:MONDO:0014751,MedGen:C4225229,OMIM:616728,Orphanet:477993]
591_ARG TER 8.3kJPN
chr1:23403829 		-
- 0.0001 -
610_THR ARG 8.3kJPN
chr1:23405516 		-
- 0.0001 -
761_TYR HIS VAR_076368 rs864309714
LP/P - Cleft palate, psychomotor retardation, and distinctive facial features (CPRF) [MIM:616728]
761_TYR HIS ClinVar
chr1:23408767 		rs864309714
Pathogenic - Palatal anomalies-widely spaced teeth-facial dysmorphism-developmental delay syndrome [MONDO:MONDO:0014751,MedGen:C4225229,OMIM:616728,Orphanet:477993]
778_GLN TER 8.3kJPN
chr1:23408818 		-
- 0.0001 -
781_THR ASN 8.3kJPN
chr1:23408828 		-
- 0.0002 -
785_SER LEU 8.3kJPN
chr1:23408840 		rs771287901
- 0.0001 -
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Reference

PiSite: a database of protein interaction sites using multiple binding states in the PDB, Miho Higurashi, Takashi Ishida and Kengo Kinoshita, Nucleic Acids Research 2009 37(Database issue):D360-D364

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