5gtc.1 | SWISS-MODEL Template Library

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SMTL ID : 5gtc.1

Crystal structure of complex between DMAP-SH conjugated with a Kaposi's sarcoma herpesvirus LANA peptide (5-15) and nucleosome core particle

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

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

Ligands

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.1:	3 residues within 4Å: Chain A: M.124, P.125, K.126 Ligand excluded by PLIP
CL.2:	7 residues within 4Å: Chain C: G.48, A.49, G.50, A.51 Chain D: T.94, S.95 Chain J: T.112 Ligand excluded by PLIP
CL.3:	2 residues within 4Å: Chain E: P.125, K.126 Ligand excluded by PLIP
CL.5:	7 residues within 4Å: Chain G: G.48, A.49, G.50, A.51 Chain H: T.94, S.95 Chain I: A.111 Ligand excluded by PLIP

6 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.4:	1 residues within 4Å: Chain E: D.81 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.81
MN.6:	2 residues within 4Å: Chain I: G.121, G.122 No protein-ligand interaction detected (PLIP)
MN.7:	2 residues within 4Å: Chain I: C.132, A.133 No protein-ligand interaction detected (PLIP)
MN.8:	2 residues within 4Å: Chain J: G.39, G.40 No protein-ligand interaction detected (PLIP)
MN.9:	2 residues within 4Å: Chain J: G.71, A.72 No protein-ligand interaction detected (PLIP)
MN.10:	2 residues within 4Å: Chain J: A.133, G.134 No protein-ligand interaction detected (PLIP)

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Amamoto, Y. et al., Synthetic Posttranslational Modifications: Chemical Catalyst-Driven Regioselective Histone Acylation of Native Chromatin. J. Am. Chem. Soc. (2017)

Release Date

2017-06-28

Peptides

Histone H3.1: AE
Histone H4: BF
Histone H2A type 1-B/E: CG
Histone H2B type 1-J: DH
LANA peptide: K

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

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Histone H3.1

Histone H4

Histone H2A type 1-B/E

Histone H2B type 1-J

LANA peptide

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