9dde.1 | SWISS-MODEL Template Library

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SMTL ID : 9dde.1

ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-1-1-1-1-1-mer

Ligands

5 x ZN: ZINC ION(Non-covalent)

ZN.1:	4 residues within 4Å: Chain K: C.18, C.21, C.39, C.42 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.18, K:C.21, K:C.39, K:C.42
ZN.2:	4 residues within 4Å: Chain K: C.34, H.36, C.53, C.56 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.34, K:H.36, K:C.53, K:C.56
ZN.3:	4 residues within 4Å: Chain L: C.51, C.54, C.72, C.75 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.51, L:C.54, L:C.72, L:C.75
ZN.4:	5 residues within 4Å: Chain L: C.67, H.69, C.87, T.89, C.90 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.67, L:H.69, L:C.87, L:C.90
ZN.5:	4 residues within 4Å: Chain M: C.27, C.30, C.41, C.44 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.27, M:C.30, M:C.41, M:C.44

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Lopez, V.G. et al., Read-write mechanisms of H2A ubiquitination by Polycomb repressive complex 1. Nature (2024)

Release Date

2024-11-20

Peptides

Histone H3.2: AE
Histone H4: BF
Histone H2A type 1: CG
Histone H2B 1.1: DH
Polycomb complex protein BMI-1: K
E3 ubiquitin-protein ligase RING2: L
RING1 and YY1-binding protein: M
Ubiquitin: N
Histone H1.4: O

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

B
B

F
F

C
C

G
G

D
D

H
H

K
K

L
L

M
M

N
N

O
O

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Histone H3.2

Histone H4

Histone H2A type 1

Toggle Identical (CG)

Histone H2B 1.1

Toggle Identical (DH)

Polycomb complex protein BMI-1

E3 ubiquitin-protein ligase RING2

RING1 and YY1-binding protein

Ubiquitin

Histone H1.4

Related Entries With Identical Sequence

1eqz.1 | 1f66.1 | 1hq3.1 | 1tzy.1 | 1u35.1 | 2aro.1 | 2cv5.1 | 2f8n.1 | 2k6d.1 | 2kjh.1 | 2n13.1 | 3lel.1 | 3lel.2 | 3nqu.1 | 3r45.1 | 4bbn.1 | 4dhj.3 | 4dhj.6 | 4dhz.2 | 4hga.1 | 4kgc.1 | 4ld9.1 | 4z2m.1 | 4zux.1 | 4zux.2 | 5bnb.1 | 5bnb.2 | 5bnb.3 | 5bnb.4 | 5c3i.1 more...less...

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