General information
PDB ID 6VYP
Title CRYSTAL STRUCTURE OF THE LSD1/COREST HISTONE DEMETHYLASE BOUND TO ITS NUCLEOSOME SUBSTRATE
PDB header NUCLEAR PROTEIN/DNA
Date 2020-02-27
Experimental method X-RAY DIFFRACTION
Resolution (A) 4.99
Kind dna
Organism XENOPUS LAEVIS, SYNTHETIC CONSTRUCT, HOMO SAPIENS
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PDB PDBe MMDB Jena OCA
CATH PDBsum HSSP PDBePISA UniProt
ProteopediA BIPA
Composition of PDB entry and biounits
File: Protein chains: DNA chains: RNA chains: No. of models: Action:
PDB entry:
pdb6vyp.pdb ABCDEFGHabcdefghMNmnKLkl IJij 0
Biounits:
6vyp.pdb1.pdb ABCDEFGHMNKL IJ 1
6vyp.pdb2.pdb abcdefghmnkl ij 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
Histone Domain P84233_2-132 4.9e-47 1 CL0012 A 3 131 IJ   
Histone Domain P84233_43-132 2.6e-44 1 CL0012 a 41 131 j   
CENP-T_C Domain P62799_26-99 4.6e-08 1 CL0012 b 26 98   
CENP-T_C Domain P62799_26-99 4.6e-08 1 CL0012 B 25 98 IJ   
Histone Domain P06897_19-91 1.2e-15 1 CL0012 c 16 90   
Histone Domain P06897_19-91 1.2e-15 1 CL0012 c 16 90   
Histone Domain P06897_19-91 1.2e-15 1 CL0012 C 16 90 IJ   
Histone Domain P06897_19-91 1.2e-15 1 CL0012 C 16 90 IJ   
Histone Domain P02281_33-102 2.9e-21 1 CL0012 D 30 98 IJ   
Histone Domain P02281_33-102 4.9e-21 1 CL0012 d 31 98 j   
Histone Domain P84233_2-132 4.1e-47 1 CL0012 E 1 131 IJ   
Histone Domain P84233_2-132 6.1e-45 1 CL0012 e 4 131 i   
CENP-T_C Domain P62799_26-99 4.2e-08 1 CL0012 f 26 98   
CENP-T_C Domain P62799_26-99 4.2e-08 1 CL0012 f 26 98   
CENP-T_C Domain P62799_26-99 4.2e-08 1 CL0012 F 26 98 IJ   
CENP-T_C Domain P62799_26-99 4.2e-08 1 CL0012 F 26 98 IJ   
Histone Domain P06897_19-91 8.9e-16 1 CL0012 G 14 90 IJ   
Histone Domain P06897_19-91 9.8e-16 1 CL0012 g 15 90   
Histone Domain P02281_33-102 1.1e-21 1 CL0012 h 29 98 i   
Histone Domain P02281_33-102 1.1e-21 1 CL0012 h 29 98 i   
Histone Domain P02281_33-102 1.1e-21 1 CL0012 H 29 98 IJ   
Histone Domain P02281_33-102 1.1e-21 1 CL0012 H 29 98 IJ   
Amino_oxidase Domain O60341_288-826 1.4e-133 1 CL0063 k 288 826 i   
Amino_oxidase Domain O60341_288-826 1.4e-133 1 CL0063 k 288 826 i   
Amino_oxidase Domain O60341_288-826 1.4e-133 1 CL0063 K 288 826 J   
Amino_oxidase Domain O60341_288-826 1.4e-133 1 CL0063 K 288 826 J   
SWIRM Domain O60341_177-264 7e-17 1 CL0123 k 177 264   
SWIRM Domain O60341_177-264 7e-17 1 CL0123 k 177 264   
SWIRM Domain O60341_177-264 7e-17 1 CL0123 K 177 264   
SWIRM Domain O60341_177-264 7e-17 1 CL0123 K 177 264   
Myb_DNA-binding Domain Q9UKL0_384-428 1.5e-10 1 CL0123 L 381 425   
Myb_DNA-binding Domain Q9UKL0_384-428 1.5e-10 1 CL0123 L 381 425   
Myb_DNA-binding Domain Q9UKL0_384-428 1.5e-10 1 CL0123 l 381 425   
Myb_DNA-binding Domain Q9UKL0_384-428 1.5e-10 1 CL0123 l 381 425   
Amino_oxidase Domain O60341_288-826 1.4e-133 1 CL0063 m 288 826 j   
Amino_oxidase Domain O60341_288-826 1.4e-133 1 CL0063 m 288 826 j   
Amino_oxidase Domain O60341_288-826 1.4e-133 1 CL0063 M 288 826 J   
Amino_oxidase Domain O60341_288-826 1.4e-133 1 CL0063 M 288 826 J   
SWIRM Domain O60341_177-264 7e-17 1 CL0123 m 177 264   
SWIRM Domain O60341_177-264 7e-17 1 CL0123 m 177 264   
SWIRM Domain O60341_177-264 7e-17 1 CL0123 M 177 264   
SWIRM Domain O60341_177-264 7e-17 1 CL0123 M 177 264   
Myb_DNA-binding Domain Q9UKL0_384-428 1.5e-10 1 CL0123 n 381 425   
Myb_DNA-binding Domain Q9UKL0_384-428 1.5e-10 1 CL0123 n 381 425   
Myb_DNA-binding Domain Q9UKL0_384-428 1.5e-10 1 CL0123 N 381 425   
Myb_DNA-binding Domain Q9UKL0_384-428 1.5e-10 1 CL0123 N 381 425   
Histone_H2A_C Family P06897_92-120 2.9e-17 1 No_clan c 91 118   
Histone_H2A_C Family P06897_92-120 2.9e-17 1 No_clan c 91 118   
Histone_H2A_C Family P06897_92-120 2.9e-17 1 No_clan C 91 118   
Histone_H2A_C Family P06897_92-120 2.9e-17 1 No_clan C 91 118   
Histone_H2A_C Family P06897_92-120 3e-17 1 No_clan g 91 118   
Histone_H2A_C Family P06897_92-120 3e-17 1 No_clan G 91 118   
SCOP domains
No SCOP domains
GO terms
Protein chains: GO type: GO description:
A/E/a/e=2-136 C nucleoplasm
A/E/a/e=2-136 C nucleosome
A/E/a/e=2-136 F DNA binding
A/E/a/e=2-136 F protein heterodimerization activity
B/F/b/f=2-103 C host cell nucleus
B/F/b/f=2-103 C nucleosome
B/F/b/f=2-103 C nucleus
B/F/b/f=2-103 F DNA binding
B/F/b/f=2-103 F protein heterodimerization activity
B/F/b/f=2-103 P DNA-templated transcription, initiation
C/G/c/g=2-130 C nucleosome
C/G/c/g=2-130 C nucleus
C/G/c/g=2-130 F DNA binding
C/G/c/g=2-130 F protein heterodimerization activity
D/H/d/h=5-126 C nucleosome
D/H/d/h=5-126 C nucleus
D/H/d/h=5-126 F DNA binding
D/H/d/h=5-126 F protein heterodimerization activity
K/M/k/m=171-852 C DNA repair complex
K/M/k/m=171-852 C nuclear chromatin
K/M/k/m=171-852 C nuclear chromosome, telomeric region
K/M/k/m=171-852 C nucleoplasm
K/M/k/m=171-852 C nucleus
K/M/k/m=171-852 C protein-containing complex
K/M/k/m=171-852 C transcription regulator complex
K/M/k/m=171-852 F androgen receptor binding
K/M/k/m=171-852 F chromatin binding
K/M/k/m=171-852 F demethylase activity
K/M/k/m=171-852 F enzyme binding
K/M/k/m=171-852 F flavin adenine dinucleotide binding
K/M/k/m=171-852 F histone demethylase activity
K/M/k/m=171-852 F histone demethylase activity (H3-dimethyl-K4 specific)
K/M/k/m=171-852 F histone demethylase activity (H3-K4 specific)
K/M/k/m=171-852 F histone demethylase activity (H3-K9 specific)
K/M/k/m=171-852 F MRF binding
K/M/k/m=171-852 F nuclear receptor transcription coactivator activity
K/M/k/m=171-852 F oxidoreductase activity
K/M/k/m=171-852 F p53 binding
K/M/k/m=171-852 F promoter-specific chromatin binding
K/M/k/m=171-852 F RNA polymerase II transcription factor binding
K/M/k/m=171-852 F telomeric repeat-containing RNA binding
K/M/k/m=171-852 F transcription factor binding
K/M/k/m=171-852 P alternative mRNA splicing, via spliceosome
K/M/k/m=171-852 P blood coagulation
K/M/k/m=171-852 P cellular response to cAMP
K/M/k/m=171-852 P cellular response to gamma radiation
K/M/k/m=171-852 P cellular response to UV
K/M/k/m=171-852 P cerebral cortex development
K/M/k/m=171-852 P guanine metabolic process
K/M/k/m=171-852 P histone H3-K4 demethylation
K/M/k/m=171-852 P histone H3-K9 demethylation
K/M/k/m=171-852 P muscle cell development
K/M/k/m=171-852 P negative regulation of DNA binding
K/M/k/m=171-852 P negative regulation of DNA damage response, signal transduction by p53 class mediator
K/M/k/m=171-852 P negative regulation of DNA-binding transcription factor activity
K/M/k/m=171-852 P negative regulation of histone H3-K4 methylation
K/M/k/m=171-852 P negative regulation of histone H3-K9 methylation
K/M/k/m=171-852 P negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
K/M/k/m=171-852 P negative regulation of protein binding
K/M/k/m=171-852 P negative regulation of transcription by RNA polymerase II
K/M/k/m=171-852 P negative regulation of transcription, DNA-templated
K/M/k/m=171-852 P neuron maturation
K/M/k/m=171-852 P positive regulation of cell size
K/M/k/m=171-852 P positive regulation of chromatin binding
K/M/k/m=171-852 P positive regulation of cold-induced thermogenesis
K/M/k/m=171-852 P positive regulation of DNA-binding transcription factor activity
K/M/k/m=171-852 P positive regulation of histone ubiquitination
K/M/k/m=171-852 P positive regulation of neural precursor cell proliferation
K/M/k/m=171-852 P positive regulation of neuroblast proliferation
K/M/k/m=171-852 P positive regulation of neuron projection development
K/M/k/m=171-852 P positive regulation of stem cell proliferation
K/M/k/m=171-852 P positive regulation of transcription by RNA polymerase II
K/M/k/m=171-852 P protein demethylation
K/M/k/m=171-852 P regulation of cellular protein localization
K/M/k/m=171-852 P regulation of double-strand break repair via homologous recombination
K/M/k/m=171-852 P regulation of transcription by RNA polymerase II
K/M/k/m=171-852 P response to fungicide
L/N/l/n=289-443 C DNA repair complex
L/N/l/n=289-443 C nucleoplasm
L/N/l/n=289-443 C nucleus
L/N/l/n=289-443 C transcription repressor complex
L/N/l/n=289-443 F DNA-binding transcription factor activity
L/N/l/n=289-443 F transcription corepressor activity
L/N/l/n=289-443 F transcription factor binding
L/N/l/n=289-443 F transcription regulatory region sequence-specific DNA binding
L/N/l/n=289-443 P blood coagulation
L/N/l/n=289-443 P histone H4 deacetylation
L/N/l/n=289-443 P negative regulation of transcription, DNA-templated
L/N/l/n=289-443 P viral process
Sequences
Download file with secondary structure created by Stride  
6vyp.pdb1.pdb:   [ download sequences in FASTA format ]
I (dna): 
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J (dna): 
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A (protein): 
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B (protein): 
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C (protein): 
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D (protein): 
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E (protein): 
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F (protein): 
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G (protein): 
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H (protein): 
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K (protein): 
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L (protein): 
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M (protein): 
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N (protein): 
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6vyp.pdb2.pdb:   [ download sequences in FASTA format ]
i (dna): 
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j (dna): 
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a (protein): 
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b (protein): 
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c (protein): 
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d (protein): 
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e (protein): 
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f (protein): 
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g (protein): 
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h (protein): 
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k (protein): 
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l (protein): 
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m (protein): 
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n (protein): 
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