SMTL ID : 9ihd.1

Nucleosome core particle bound by one molecule of DTT-reduced native monomeric myeloperoxidase

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.97 Å

Oligo State

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

Ligands

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.1: 18 residues within 4Å: Chain K: M.89, G.92, Q.93, D.96, D.100, F.101 Chain L: R.127, M.131, T.217, F.220, R.221, G.223, H.224, I.227, F.253, L.294, L.305, N.309 12 PLIP interactions: 11 interactions with chain L, 1 interactions with chain K, Hydrophobic interactions: L:F.220, L:I.227, L:F.253, L:L.294, L:L.305, L:L.305, K:Q.93 Salt bridges: L:R.221, L:H.224 pi-Cation interactions: L:R.221, L:H.224 Metal complexes: L:H.224

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Post Translational Modification)

NAG.2: 4 residues within 4Å: Chain L: N.113, S.115, A.116, W.257 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:N.113 NAG.3: 5 residues within 4Å: Chain L: N.77, N.80, L.82, L.84, Q.89 4 PLIP interactions: 4 interactions with chain L Hydrophobic interactions: L:L.82, L:L.84 Hydrogen bonds: L:N.77, L:Q.89 NAG.4: 2 residues within 4Å: Chain L: N.205, V.208 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:N.205

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Burn, G.L. et al., Myeloperoxidase transforms chromatin into Neutrophil Extracellular Traps. To Be Published

Release Date

2025-08-06

Peptides

Histone H3.2: AE
Histone H4: BF
Histone H2A type 1: CG
Histone H2B 1.1: DH
Myeloperoxidase light chain: K
Myeloperoxidase light chain: L

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
M

L
N

Histone H3.2

Histone H4

Histone H2A type 1

Histone H2B 1.1

Myeloperoxidase light chain

Myeloperoxidase light chain

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