SMTL ID : 9ihe.1

Nucleosome core particle bound by two molecules of DTT-reduced native monomeric myeloperoxidase

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.95 Å

Oligo State

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

Ligands

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 19 residues within 4Å: Chain K: M.89, G.92, Q.93, D.96, D.100, T.102 Chain L: E.130, M.131, T.217, F.220, R.221, G.223, H.224, I.227, F.253, L.294, F.295, L.305, R.312 14 PLIP interactions: 12 interactions with chain L, 2 interactions with chain K, Hydrophobic interactions: L:R.221, L:I.227, L:F.253, L:L.294, L:L.294, L:F.295, L:L.305, L:L.305, K:Q.93 Salt bridges: L:R.221, L:R.221, L:R.312 Metal complexes: L:H.224 Hydrogen bonds: K:T.102 HEM.5: 18 residues within 4Å: Chain M: M.89, G.92, Q.93, D.96, T.102 Chain N: M.131, T.217, F.220, R.221, G.223, H.224, I.227, F.253, L.294, F.295, L.305, L.308, R.312 13 PLIP interactions: 11 interactions with chain N, 2 interactions with chain M, Hydrophobic interactions: N:R.221, N:I.227, N:I.227, N:F.253, N:L.294, N:F.295, N:L.305, M:Q.93 Salt bridges: N:R.221, N:R.221, N:R.312 Metal complexes: N:H.224 Hydrogen bonds: M:T.102

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.2: 4 residues within 4Å: Chain L: N.113, A.116, W.257, L.261 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:N.113 NAG.3: 8 residues within 4Å: Chain L: N.77, S.79, N.80, L.84, L.85, A.86, V.87, Q.89 6 PLIP interactions: 6 interactions with chain L Hydrophobic interactions: L:L.84 Hydrogen bonds: L:N.77, L:S.79, L:N.80, L:V.87, L:Q.89 NAG.4: 3 residues within 4Å: Chain L: R.202, N.205, S.207 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:R.202, L:N.205 NAG.6: 3 residues within 4Å: Chain N: N.113, S.115, W.257 2 PLIP interactions: 2 interactions with chain N Hydrogen bonds: N:N.113, N:S.115 NAG.7: 5 residues within 4Å: Chain N: N.77, S.79, N.80, L.84, Q.89 5 PLIP interactions: 5 interactions with chain N Hydrophobic interactions: N:L.84 Hydrogen bonds: N:N.77, N:S.79, N:N.80, N:Q.89 NAG.8: 2 residues within 4Å: Chain N: N.205, S.207 1 PLIP interactions: 1 interactions with chain N Hydrogen bonds: N: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: KM
Myeloperoxidase light chain: LN

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

M
M

L
L

N
N

Histone H3.2

Histone H4

Histone H2A type 1

Histone H2B 1.1

Myeloperoxidase light chain

Myeloperoxidase light chain

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