SMTL ID : 9ihf.1

Nucleosome core particle bound by one monomer and one dimer of of DTT-reduced native myeloperoxidase

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.16 Å

Oligo State

hetero-2-2-2-2-3-3-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- FUC: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-FUC.1: 15 residues within 4Å: Chain N: N.205, S.207, V.208, R.392, K.393 Chain O: W.34, L.35 Chain P: K.196, R.326, F.327, C.328, G.329, C.385, K.393 Ligands: NAG-NAG-BMA-MAN-FUC.2 3 PLIP interactions: 1 interactions with chain N, 1 interactions with chain P, 1 interactions with chain O Hydrophobic interactions: N:V.208, N:R.392, N:K.393, O:L.35 Hydrogen bonds: N:K.393, P:K.393, O:W.34, N:S.207

1 x NAG- NAG- BMA- MAN- FUC: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-FUC.2: 12 residues within 4Å: Chain M: W.34 Chain N: R.326, F.327, C.328, G.329, T.389, K.393 Chain P: N.205, S.207, V.208, K.393 Ligands: NAG-NAG-BMA-MAN-MAN-FUC.1 4 PLIP interactions: 2 interactions with chain P, 2 interactions with chain N Hydrophobic interactions: P:V.208 Hydrogen bonds: P:K.393, N:K.393, N:K.393

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

HEM.3: 20 residues within 4Å: Chain K: M.89, G.92, Q.93, D.96, 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, L.308, N.309, R.312 13 PLIP interactions: 11 interactions with chain L, 2 interactions with chain K, Hydrophobic interactions: L:F.220, L:F.220, L:I.227, L:F.253, L:L.294, L:F.295, 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.7: 20 residues within 4Å: Chain M: M.89, G.92, Q.93, D.96, D.100, F.101, 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 15 PLIP interactions: 10 interactions with chain N, 5 interactions with chain M, Hydrophobic interactions: N:R.221, N:I.227, N:F.253, N:L.294, N:F.295, N:L.305, M:Q.93, M:Q.93 Salt bridges: N:R.221, N:R.221, N:R.312 Metal complexes: N:H.224 Hydrogen bonds: M:D.100, M:D.100, M:T.102 HEM.10: 21 residues within 4Å: Chain O: M.89, G.92, Q.93, D.96, D.100, T.102 Chain P: E.130, M.131, Y.184, T.217, F.220, R.221, G.223, H.224, I.227, F.253, L.294, F.295, L.305, L.308, R.312 15 PLIP interactions: 4 interactions with chain O, 11 interactions with chain P, Hydrophobic interactions: O:Q.93, P:R.221, P:I.227, P:I.227, P:F.253, P:L.294, P:F.295, P:L.305 Hydrogen bonds: O:D.100, O:D.100, O:T.102 Salt bridges: P:R.221, P:R.221, P:R.312 Metal complexes: P:H.224

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

NAG.4: 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.5: 7 residues within 4Å: Chain L: N.77, S.79, L.84, L.85, V.87, Q.89, N.146 4 PLIP interactions: 4 interactions with chain L Hydrophobic interactions: L:L.84 Hydrogen bonds: L:S.79, L:Q.89, L:N.146 NAG.6: 3 residues within 4Å: Chain L: N.205, S.207, V.208 No protein-ligand interaction detected (PLIP) NAG.8: 4 residues within 4Å: Chain N: N.113, S.115, W.257, L.261 2 PLIP interactions: 2 interactions with chain N Hydrogen bonds: N:N.113, N:S.115 NAG.9: 4 residues within 4Å: Chain N: N.77, S.79, L.84, N.146 No protein-ligand interaction detected (PLIP) NAG.11: 3 residues within 4Å: Chain P: N.113, W.257, L.261 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:N.113 NAG.12: 3 residues within 4Å: Chain P: N.77, N.80, Q.89 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:Q.89

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: KMO
Myeloperoxidase light chain: LNP

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

O
O

L
L

N
N

P
P

Histone H3.2

Histone H4

Histone H2A type 1

Histone H2B 1.1

Myeloperoxidase light chain

Myeloperoxidase light chain

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