6G0L
Structure of two molecules of the chromatin remodelling enzyme Chd1 bound to a nucleosome
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000786 | cellular_component | nucleosome |
| A | 0003677 | molecular_function | DNA binding |
| A | 0005634 | cellular_component | nucleus |
| A | 0005694 | cellular_component | chromosome |
| A | 0030527 | molecular_function | structural constituent of chromatin |
| A | 0031492 | molecular_function | nucleosomal DNA binding |
| A | 0031507 | biological_process | heterochromatin formation |
| A | 0046982 | molecular_function | protein heterodimerization activity |
| B | 0000786 | cellular_component | nucleosome |
| B | 0003677 | molecular_function | DNA binding |
| B | 0005515 | molecular_function | protein binding |
| B | 0005634 | cellular_component | nucleus |
| B | 0005694 | cellular_component | chromosome |
| B | 0006334 | biological_process | nucleosome assembly |
| B | 0030527 | molecular_function | structural constituent of chromatin |
| B | 0031507 | biological_process | heterochromatin formation |
| B | 0046982 | molecular_function | protein heterodimerization activity |
| C | 0000786 | cellular_component | nucleosome |
| C | 0003677 | molecular_function | DNA binding |
| C | 0005634 | cellular_component | nucleus |
| C | 0005694 | cellular_component | chromosome |
| C | 0030527 | molecular_function | structural constituent of chromatin |
| C | 0031507 | biological_process | heterochromatin formation |
| C | 0046982 | molecular_function | protein heterodimerization activity |
| D | 0000786 | cellular_component | nucleosome |
| D | 0003677 | molecular_function | DNA binding |
| D | 0030527 | molecular_function | structural constituent of chromatin |
| D | 0046982 | molecular_function | protein heterodimerization activity |
| E | 0000786 | cellular_component | nucleosome |
| E | 0003677 | molecular_function | DNA binding |
| E | 0005634 | cellular_component | nucleus |
| E | 0005694 | cellular_component | chromosome |
| E | 0030527 | molecular_function | structural constituent of chromatin |
| E | 0031492 | molecular_function | nucleosomal DNA binding |
| E | 0031507 | biological_process | heterochromatin formation |
| E | 0046982 | molecular_function | protein heterodimerization activity |
| F | 0000786 | cellular_component | nucleosome |
| F | 0003677 | molecular_function | DNA binding |
| F | 0005515 | molecular_function | protein binding |
| F | 0005634 | cellular_component | nucleus |
| F | 0005694 | cellular_component | chromosome |
| F | 0006334 | biological_process | nucleosome assembly |
| F | 0030527 | molecular_function | structural constituent of chromatin |
| F | 0031507 | biological_process | heterochromatin formation |
| F | 0046982 | molecular_function | protein heterodimerization activity |
| G | 0000786 | cellular_component | nucleosome |
| G | 0003677 | molecular_function | DNA binding |
| G | 0005634 | cellular_component | nucleus |
| G | 0005694 | cellular_component | chromosome |
| G | 0030527 | molecular_function | structural constituent of chromatin |
| G | 0031507 | biological_process | heterochromatin formation |
| G | 0046982 | molecular_function | protein heterodimerization activity |
| H | 0000786 | cellular_component | nucleosome |
| H | 0003677 | molecular_function | DNA binding |
| H | 0030527 | molecular_function | structural constituent of chromatin |
| H | 0046982 | molecular_function | protein heterodimerization activity |
| M | 0000123 | cellular_component | histone acetyltransferase complex |
| M | 0000124 | cellular_component | SAGA complex |
| M | 0000166 | molecular_function | nucleotide binding |
| M | 0000182 | molecular_function | rDNA binding |
| M | 0000724 | biological_process | double-strand break repair via homologous recombination |
| M | 0000729 | biological_process | DNA double-strand break processing |
| M | 0000785 | cellular_component | chromatin |
| M | 0000976 | molecular_function | transcription cis-regulatory region binding |
| M | 0001178 | biological_process | regulation of transcriptional start site selection at RNA polymerase II promoter |
| M | 0003677 | molecular_function | DNA binding |
| M | 0003682 | molecular_function | chromatin binding |
| M | 0005515 | molecular_function | protein binding |
| M | 0005524 | molecular_function | ATP binding |
| M | 0005634 | cellular_component | nucleus |
| M | 0005739 | cellular_component | mitochondrion |
| M | 0006325 | biological_process | chromatin organization |
| M | 0006338 | biological_process | chromatin remodeling |
| M | 0006351 | biological_process | DNA-templated transcription |
| M | 0006357 | biological_process | regulation of transcription by RNA polymerase II |
| M | 0006363 | biological_process | termination of RNA polymerase I transcription |
| M | 0006366 | biological_process | transcription by RNA polymerase II |
| M | 0006368 | biological_process | transcription elongation by RNA polymerase II |
| M | 0006369 | biological_process | termination of RNA polymerase II transcription |
| M | 0007062 | biological_process | sister chromatid cohesion |
| M | 0008094 | molecular_function | ATP-dependent activity, acting on DNA |
| M | 0010468 | biological_process | regulation of gene expression |
| M | 0016787 | molecular_function | hydrolase activity |
| M | 0016887 | molecular_function | ATP hydrolysis activity |
| M | 0030874 | cellular_component | nucleolar chromatin |
| M | 0031490 | molecular_function | chromatin DNA binding |
| M | 0034728 | biological_process | nucleosome organization |
| M | 0035861 | cellular_component | site of double-strand break |
| M | 0042393 | molecular_function | histone binding |
| M | 0046695 | cellular_component | SLIK (SAGA-like) complex |
| M | 0140002 | molecular_function | histone H3K4me3 reader activity |
| M | 0140658 | molecular_function | ATP-dependent chromatin remodeler activity |
| M | 0140750 | molecular_function | nucleosome array spacer activity |
| M | 1902275 | biological_process | regulation of chromatin organization |
| M | 2000104 | biological_process | negative regulation of DNA-templated DNA replication |
| W | 0000123 | cellular_component | histone acetyltransferase complex |
| W | 0000124 | cellular_component | SAGA complex |
| W | 0000166 | molecular_function | nucleotide binding |
| W | 0000182 | molecular_function | rDNA binding |
| W | 0000724 | biological_process | double-strand break repair via homologous recombination |
| W | 0000729 | biological_process | DNA double-strand break processing |
| W | 0000785 | cellular_component | chromatin |
| W | 0000976 | molecular_function | transcription cis-regulatory region binding |
| W | 0001178 | biological_process | regulation of transcriptional start site selection at RNA polymerase II promoter |
| W | 0003677 | molecular_function | DNA binding |
| W | 0003682 | molecular_function | chromatin binding |
| W | 0005515 | molecular_function | protein binding |
| W | 0005524 | molecular_function | ATP binding |
| W | 0005634 | cellular_component | nucleus |
| W | 0005739 | cellular_component | mitochondrion |
| W | 0006325 | biological_process | chromatin organization |
| W | 0006338 | biological_process | chromatin remodeling |
| W | 0006351 | biological_process | DNA-templated transcription |
| W | 0006357 | biological_process | regulation of transcription by RNA polymerase II |
| W | 0006363 | biological_process | termination of RNA polymerase I transcription |
| W | 0006366 | biological_process | transcription by RNA polymerase II |
| W | 0006368 | biological_process | transcription elongation by RNA polymerase II |
| W | 0006369 | biological_process | termination of RNA polymerase II transcription |
| W | 0007062 | biological_process | sister chromatid cohesion |
| W | 0008094 | molecular_function | ATP-dependent activity, acting on DNA |
| W | 0010468 | biological_process | regulation of gene expression |
| W | 0016787 | molecular_function | hydrolase activity |
| W | 0016887 | molecular_function | ATP hydrolysis activity |
| W | 0030874 | cellular_component | nucleolar chromatin |
| W | 0031490 | molecular_function | chromatin DNA binding |
| W | 0034728 | biological_process | nucleosome organization |
| W | 0035861 | cellular_component | site of double-strand break |
| W | 0042393 | molecular_function | histone binding |
| W | 0046695 | cellular_component | SLIK (SAGA-like) complex |
| W | 0140002 | molecular_function | histone H3K4me3 reader activity |
| W | 0140658 | molecular_function | ATP-dependent chromatin remodeler activity |
| W | 0140750 | molecular_function | nucleosome array spacer activity |
| W | 1902275 | biological_process | regulation of chromatin organization |
| W | 2000104 | biological_process | negative regulation of DNA-templated DNA replication |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 12 |
| Details | binding site for residue ADP M 1501 |
| Chain | Residue |
| M | GLU375 |
| M | MET781 |
| M | ARG807 |
| M | BEF1502 |
| M | LEU376 |
| M | ARG377 |
| M | GLY406 |
| M | LYS407 |
| M | THR408 |
| M | VAL409 |
| M | TRP447 |
| M | ASN779 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | binding site for residue BEF M 1502 |
| Chain | Residue |
| M | MET403 |
| M | LYS407 |
| M | GLU514 |
| M | ARG804 |
| M | ARG807 |
| M | ADP1501 |
| site_id | AC3 |
| Number of Residues | 3 |
| Details | binding site for residue BEF W 1501 |
| Chain | Residue |
| W | THR436 |
| W | ARG804 |
| W | ADP1502 |
| site_id | AC4 |
| Number of Residues | 8 |
| Details | binding site for residue ADP W 1502 |
| Chain | Residue |
| W | LEU376 |
| W | GLN380 |
| W | GLY404 |
| W | GLY406 |
| W | ASN779 |
| W | MET781 |
| W | ARG807 |
| W | BEF1501 |
| site_id | AC5 |
| Number of Residues | 8 |
| Details | binding site for Di-nucleotide DG I -3 and DC I -2 |
| Chain | Residue |
| A | ARG116 |
| A | VAL117 |
| A | THR118 |
| I | DC-4 |
| I | DG-1 |
| J | DG2 |
| J | DC3 |
| J | DG4 |
| site_id | AC6 |
| Number of Residues | 8 |
| Details | binding site for Di-nucleotide DC I 21 and SER W 524 |
| Chain | Residue |
| I | DG20 |
| I | DC22 |
| J | DG-21 |
| W | GLU522 |
| W | SER523 |
| W | LEU525 |
| W | TYR526 |
| W | SER528 |
| site_id | AC7 |
| Number of Residues | 10 |
| Details | binding site for Di-nucleotide DC I 22 and ASN W 520 |
| Chain | Residue |
| I | DC21 |
| I | DA23 |
| J | DG-21 |
| J | DG-22 |
| W | LEU518 |
| W | LYS519 |
| W | ALA521 |
| W | GLU522 |
| W | SER523 |
| W | LYS550 |
| site_id | AC8 |
| Number of Residues | 6 |
| Details | binding site for Di-nucleotide DC I 45 and DA I 46 |
| Chain | Residue |
| G | LYS15 |
| I | DC44 |
| I | DG47 |
| J | DG-44 |
| J | DT-46 |
| J | DG-45 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | binding site for Di-nucleotide DC I 45 and DA I 46 |
| Chain | Residue |
| G | LYS15 |
| I | DC44 |
| I | DG47 |
| J | DG-44 |
| J | DT-46 |
| J | DG-45 |
| site_id | AD1 |
| Number of Residues | 6 |
| Details | binding site for Di-nucleotide DC I 45 and DA I 46 |
| Chain | Residue |
| G | LYS15 |
| I | DC44 |
| I | DG47 |
| J | DG-44 |
| J | DT-46 |
| J | DG-45 |
| site_id | AD2 |
| Number of Residues | 6 |
| Details | binding site for Di-nucleotide DC I 45 and DA I 46 |
| Chain | Residue |
| G | LYS15 |
| I | DC44 |
| I | DG47 |
| J | DG-44 |
| J | DT-46 |
| J | DG-45 |
| site_id | AD3 |
| Number of Residues | 6 |
| Details | binding site for Di-nucleotide DC I 45 and DA I 46 |
| Chain | Residue |
| G | LYS15 |
| I | DC44 |
| I | DG47 |
| J | DG-44 |
| J | DT-46 |
| J | DG-45 |
| site_id | AD4 |
| Number of Residues | 6 |
| Details | binding site for Di-nucleotide DC I 45 and DA I 46 |
| Chain | Residue |
| G | LYS15 |
| I | DC44 |
| I | DG47 |
| J | DG-44 |
| J | DT-46 |
| J | DG-45 |
| site_id | AD5 |
| Number of Residues | 6 |
| Details | binding site for Di-nucleotide DC I 45 and DA I 46 |
| Chain | Residue |
| G | LYS15 |
| I | DC44 |
| I | DG47 |
| J | DG-44 |
| J | DT-46 |
| J | DG-45 |
| site_id | AD6 |
| Number of Residues | 6 |
| Details | binding site for Di-nucleotide DC I 45 and DA I 46 |
| Chain | Residue |
| I | DG47 |
| J | DG-44 |
| J | DT-46 |
| J | DG-45 |
| G | LYS15 |
| I | DC44 |
| site_id | AD7 |
| Number of Residues | 9 |
| Details | binding site for Di-nucleotide DG I -53 and DT J 54 |
| Chain | Residue |
| D | LYS43 |
| I | DA-54 |
| I | DG-52 |
| I | DT53 |
| I | DT55 |
| J | DC-52 |
| J | DC-54 |
| J | DC53 |
| J | DT55 |
| site_id | AD8 |
| Number of Residues | 10 |
| Details | binding site for Di-nucleotide DT J -17 and GLU W 493 |
| Chain | Residue |
| I | DA16 |
| J | DT-16 |
| J | DG-18 |
| W | LEU434 |
| W | THR491 |
| W | TYR492 |
| W | TYR494 |
| W | ILE495 |
| W | LEU496 |
| W | LYS497 |
| site_id | AD9 |
| Number of Residues | 12 |
| Details | binding site for Di-nucleotide DG J -18 and GLU W 493 |
| Chain | Residue |
| I | DA17 |
| I | DC18 |
| I | DC19 |
| J | DT-17 |
| J | DG-19 |
| J | DT-16 |
| W | THR491 |
| W | TYR492 |
| W | TYR494 |
| W | ILE495 |
| W | LEU496 |
| W | LYS497 |
Functional Information from PROSITE/UniProt
| site_id | PS00046 |
| Number of Residues | 7 |
| Details | HISTONE_H2A Histone H2A signature. AGLqFPV |
| Chain | Residue | Details |
| C | ALA21-VAL27 | |
| G | ALA21-VAL27 |
| site_id | PS00047 |
| Number of Residues | 5 |
| Details | HISTONE_H4 Histone H4 signature. GAKRH |
| Chain | Residue | Details |
| B | GLY14-HIS18 |
| site_id | PS00322 |
| Number of Residues | 7 |
| Details | HISTONE_H3_1 Histone H3 signature 1. KAPRKQL |
| Chain | Residue | Details |
| A | LYS14-LEU20 |
| site_id | PS00357 |
| Number of Residues | 23 |
| Details | HISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG |
| Chain | Residue | Details |
| D | ARG89-GLY111 |
| site_id | PS00598 |
| Number of Residues | 21 |
| Details | CHROMO_1 Chromo domain signature. FlIKWtDEshlhn.TWETyesI |
| Chain | Residue | Details |
| M | PHE213-ILE233 | |
| M | TYR307-ILE327 |
| site_id | PS00959 |
| Number of Residues | 9 |
| Details | HISTONE_H3_2 Histone H3 signature 2. PFqRLVREI |
| Chain | Residue | Details |
| A | PRO66-ILE74 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 3 |
| Details | Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 4 |
| Details | Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 5 |
| Details | Modified residue: {"description":"N6-propionyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Phosphoserine; by PAK2","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 4 |
| Details | Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI8 |
| Number of Residues | 2 |
| Details | Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in UFM1); alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI9 |
| Number of Residues | 4 |
| Details | Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI10 |
| Number of Residues | 4 |
| Details | DNA binding: {} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI11 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-(2-hydroxyisobutyryl)lysine; alternate","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI12 |
| Number of Residues | 4 |
| Details | Modified residue: {"description":"N6-(2-hydroxyisobutyryl)lysine","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI13 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI14 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N5-methylglutamine","evidences":[{"evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI15 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI16 |
| Number of Residues | 2 |
| Details | Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI17 |
| Number of Residues | 130 |
| Details | Domain: {"description":"Chromo 2","evidences":[{"source":"PROSITE-ProRule","id":"PRU00053","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI18 |
| Number of Residues | 6 |
| Details | Motif: {"description":"DEAH box"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI19 |
| Number of Residues | 14 |
| Details | Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00541","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI20 |
| Number of Residues | 4 |
| Details | Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"12872131","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI21 |
| Number of Residues | 174 |
| Details | Domain: {"description":"Helicase ATP-binding","evidences":[{"source":"PROSITE-ProRule","id":"PRU00541","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
