PDB ID 2V1D     CHAIN A
Protein name LYSINE-SPECIFIC HISTONE DEMETHYLASE 1
Uniprot Accession O60341
The number of similar proteins 120
The number of binding states 5
The number of binding partners 4

Coloring

Unicolor (beige)

The number of binding partners

Group

Binding
state		 Binding partners
2V1D (CHAIN: A)
1 Q9UKL0  
2 Monomeric state
3 Q9UKL0  
4 Q9UKL0   Q01101  
5 Q9UKL0   A0A310TTQ1  

Downdload

Format:

Molecule viewer


Only interaction residues
#binding
partners
  4
  3
  2
  1
  0

Sequence information

1   MDESLANLSE   DEYYSEEERN   AKAEKEKKLP   PPPPQAPPEE   ENESEPEEPS   50
51   GVEGAAFQSR   LPHDRMTSQE   AACFPDIISG   PQQTQKVFLF   IRNRTLQLWL   100
101   DNPKIQLTFE   ATLQQLEAPY   NSDTVLVHRV   HSYLERHGLI   NFGIYKRIKP   150
151   LPTKKTGKVI   IIGSGVSGLA   AARQLQSFGM   DVTLLEARDR   VGGRVATFRK   200
201   GNYVADLGAM   VVTGLGGNPM   AVVSKQVNME   LAKIKQKCPL   YEANGQAVPK   250
251   EKDEMVEQEF   NRLLEATSYL   SHQLDFNVLN   NKPVSLGQAL   EVVIQLQEKH   300
301   VKDEQIEHWK   KIVKTQEELK   ELLNKMVNLK   EKIKELHQQY   KEASEVKPPR   350
351   DITAEFLVKS   KHRDLTALCK   EYDELAETQG   KLEEKLQELE   ANPPSDVYLS   400
401   SRDRQILDWH   FANLEFANAT   PLSTLSLKHW   DQDDDFEFTG   SHLTVRNGYS   450
451   CVPVALAEGL   DIKLNTAVRQ   VRYTASGCEV   IAVNTRSTSQ   TFIYKCDAVL   500
501   CTLPLGVLKQ   QPPAVQFVPP   LPEWKTSAVQ   RMGFGNLNKV   VLCFDRVFWD   550
551   PSVNLFGHVG   STTASRGELF   LFWNLYKAPI   LLALVAGEAA   GIMENISDDV   600
601   IVGRCLAILK   GIFGSSAVPQ   PKETVVSRWR   ADPWARGSYS   YVAAGSSGND   650
651   YDLMAQPITP   GPSIPGAPQP   IPRLFFAGEH   TIRNYPATVH   GALLSGLREA   700
701   GRIADQFLGA   MYTLPRQATP   GVPAQQSPSM       750

Variants

Residue AA Source /
dbSNP		 Clinical
Significance
 Allele
Frequency
(> 0.0001)		 AlphaMissense
pathogenicity		 Disease name
177_ALA SER 8.3kJPN
chr1:23376891
rs765222197
- 0.0001 0.5064 -
251_ARG TER ClinVar
chr1:23381582
-
Pathogenic - - ACTH-independent macronodular adrenal hyperplasia 3 [MONDO:MONDO:0700299,MedGen:C5975485,OMIM:620990]
254_SER GLY 8.3kJPN
chr1:23381591
rs532200849
- 0.0003 0.085 -
260_GLY ARG VAR_090104
-
US - - ACTH-independent macronodular adrenal hyperplasia 3 (AIMAH3) [MIM:620990]
289_SER PRO VAR_090106
-
US - - ACTH-independent macronodular adrenal hyperplasia 3 (AIMAH3) [MIM:620990]
315_GLY TER ClinVar
chr1:23383989
rs1553129293
Likely pathogenic - - not provided [MedGen:CN517202]
332_MET VAL 8.3kJPN
chr1:23384040
-
- 0.0001 0.9724 -
344_VAL LEU 8.3kJPN
chr1:23385583
-
- 0.0001 0.9096 -
375_ASP GLY ClinVar
chr1:23395048
rs1553130904
Likely pathogenic - 0.9998 not provided|Intellectual disability [MedGen:C3661900|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 0.9005 -
379_GLU LYS VAR_076366
rs864309715
LP/P - 0.9998 Cleft palate, psychomotor retardation, and distinctive facial features (CPRF) [MIM:616728]
379_GLU LYS ClinVar
chr1:23395059
rs864309715
Pathogenic - 0.9998 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 - 0.9985 not provided [MedGen:C3661900]
451_LEU TRP 8.3kJPN
chr1:23397728
rs769906942
- 0.0002 0.631 -
471_PRO SER 8.3kJPN
chr1:23397787
-
- 0.0001 0.9285 -
489_ALA THR 8.3kJPN
chr1:23397841
rs758354898
- 0.0001 0.1175 -
520_TYR CYS 8.3kJPN
chr1:23399793
-
- 0.0001 0.9997 -
554_GLN ARG ClinVar
chr1:23399895
rs2124523419
Likely pathogenic - 0.9988 Neurodevelopmental delay|Palatal anomalies-widely spaced teeth-facial dysmorphism-developmental delay syndrome|Squamous cell lung carcinoma [Human Phenotype Ontology:HP:0012758,MedGen:C4022738|MONDO:MONDO:0014751,MedGen:C4225229,OMIM:616728,Orphanet:477993|MedGen:C0149782]
555_ASP GLY ClinVar
chr1:23403722
rs2124538211
Likely pathogenic - 0.9998 not provided [MedGen:C3661900]
555_ASP VAL ClinVar
chr1:23403722
rs2124538211
Likely pathogenic - 0.9999 not provided [MedGen:C3661900]
556_ASP GLY VAR_076367
rs864309716
LP/P - 0.9994 Cleft palate, psychomotor retardation, and distinctive facial features (CPRF) [MIM:616728]
556_ASP GLY ClinVar
chr1:23403725
rs864309716
Pathogenic - 0.9994 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 0.8599 -
638_GLN TER ClinVar
chr1:23405599
-
Pathogenic - - ACTH-independent macronodular adrenal hyperplasia 3 [MONDO:MONDO:0700299,MedGen:C5975485,OMIM:620990]
761_TYR HIS VAR_076368
rs864309714
LP/P - 1.0 Cleft palate, psychomotor retardation, and distinctive facial features (CPRF) [MIM:616728]
761_TYR HIS ClinVar
chr1:23408767
rs864309714
Pathogenic - 1.0 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 0.3349 -
785_SER LEU 8.3kJPN
chr1:23408840
rs771287901
- 0.0001 0.1319 -
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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

COPYRIGHTc2008-2019 Miho Higurashi, Takashi Ishida and Kengo Kinoshita. All rights reserved.