Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3UT9

Crystal Structure of Nucleosome Core Particle Assembled with a Palindromic Widom '601' Derivative (NCP-601L)

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000786	cellular_component	nucleosome
A	0003677	molecular_function	DNA binding
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005694	cellular_component	chromosome
A	0030527	molecular_function	structural constituent of chromatin
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	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	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005694	cellular_component	chromosome
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	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005654	cellular_component	nucleoplasm
E	0005694	cellular_component	chromosome
E	0030527	molecular_function	structural constituent of chromatin
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	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	0005515	molecular_function	protein binding
H	0005634	cellular_component	nucleus
H	0005694	cellular_component	chromosome
H	0030527	molecular_function	structural constituent of chromatin
H	0046982	molecular_function	protein heterodimerization activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CL C 1102

Chain	Residue
C	ALA45
C	GLY46
D	THR87
D	SER88

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MN E 1001

Chain	Residue
F	HOH115
D	VAL45
E	ASP77
E	HOH145
E	HOH146
E	HOH150

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CL G 1101

Chain	Residue
G	GLY44
G	GLY46
G	ALA47
H	THR87
H	SER88

site_id	AC4
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN I 1003

Chain	Residue
I	DG-61

site_id	AC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MN I 1005

Chain	Residue
I	DG-3
I	DG-2

site_id	AC6
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN I 1006

Chain	Residue
I	DG38

site_id	AC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MN I 1007

Chain	Residue
I	DG50
I	DG51
I	HOH134

site_id	AC8
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN I 1011

Chain	Residue
I	DG-34

site_id	AC9
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN I 1013

Chain	Residue
I	DG29

site_id	BC1
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN I 1014

Chain	Residue
I	DG-49

site_id	BC2
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN I 1016

Chain	Residue
I	DG-53

site_id	BC3
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN I 1018

Chain	Residue
I	DG27

site_id	BC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MN I 1021

Chain	Residue
I	DG20
I	HOH132

site_id	BC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MN I 1023

Chain	Residue
I	DG62
I	DG63

site_id	BC6
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN I 1028

Chain	Residue
I	DC3

site_id	BC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE K I 1052

Chain	Residue
I	DT-26
I	DA-25

site_id	BC8
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN J 1002

Chain	Residue
J	DG-3

site_id	BC9
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MN J 1004

Chain	Residue
J	DG-34
J	HOH106

site_id	CC1
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN J 1008

Chain	Residue
J	DG50

site_id	CC2
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN J 1009

Chain	Residue
J	DG27

site_id	CC3
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MN J 1010

Chain	Residue
J	DG62
J	HOH129

site_id	CC4
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN J 1012

Chain	Residue
J	DG38

site_id	CC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MN J 1015

Chain	Residue
J	DG20
J	DG21

site_id	CC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MN J 1017

Chain	Residue
J	DC-62
J	DG-61

site_id	CC7
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN J 1020

Chain	Residue
J	DG-49

site_id	CC8
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN J 1022

Chain	Residue
J	DG-53

site_id	CC9
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN J 1024

Chain	Residue
J	DG29

site_id	DC1
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN J 1025

Chain	Residue
J	DA36

site_id	DC2
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN J 1026

Chain	Residue
J	DG63

site_id	DC3
Number of Residues	2
Details	BINDING SITE FOR RESIDUE K J 1051

Chain	Residue
J	DA-25
J	DT-26

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

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	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	2
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"Q71DI3","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":"P84228","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	2
Details	Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	4
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	2
Details	Modified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	2
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	2
Details	Lipidation: {"description":"S-palmitoyl cysteine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
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_FI11
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_FI12
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_FI13
Number of Residues	4
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI14
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_FI15
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_FI16
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_FI17
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_FI18
Number of Residues	4
Details	DNA binding: {}

Chain

Residue

Details

site_id	SWS_FT_FI19
Number of Residues	1
Details	Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI20
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_FI21
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_FI22
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_FI23
Number of Residues	2
Details	Modified residue: {"description":"N5-methylglutamine","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI24
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_FI25
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_FI26
Number of Residues	2
Details	Glycosylation: {"description":"O-linked (GlcNAc) serine","evidences":[{"source":"UniProtKB","id":"P62807","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI27
Number of Residues	4
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"UniProtKB","id":"P0C1H4","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)