SMTL ID : 9geq.1

Native dimeric Myeloperoxidase bound to nucleosome core particle; composite map

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

2 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: 14 residues within 4Å: Chain L: N.205, S.207, V.208, R.392 Chain M: L.35 Chain N: K.196, R.326, F.327, C.328, G.329, T.389, K.393 Ligands: NAG-NAG-BMA-MAN-MAN-FUC.2, NAG-NAG-BMA-MAN-MAN-FUC.2 4 PLIP interactions: 2 interactions with chain L, 1 interactions with chain N, 1 interactions with chain M Hydrophobic interactions: L:V.208, L:R.392, M:L.35 Hydrogen bonds: N:K.393 NAG-NAG-BMA-MAN-MAN-FUC.2: 17 residues within 4Å: Chain K: L.35 Chain L: K.196, R.326, F.327, C.328, G.329, C.385, T.389, K.393 Chain N: R.202, N.205, S.207, V.208, R.392, K.393 Ligands: NAG-NAG-BMA-MAN-MAN-FUC.1, NAG-NAG-BMA-MAN-MAN-FUC.1 5 PLIP interactions: 3 interactions with chain N, 1 interactions with chain L, 1 interactions with chain K Hydrophobic interactions: N:V.208, N:K.393, K:L.35 Hydrogen bonds: N:K.393, L:K.393

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

CL.3: 5 residues within 4Å: Chain K: R.33, W.34 Chain L: N.214, V.215, W.324 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain M: R.33, W.34 Chain N: N.214, V.215, W.324 Ligand excluded by PLIP

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.4: 16 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.295, L.308, R.312 11 PLIP interactions: 9 interactions with chain L, 2 interactions with chain K, Hydrophobic interactions: L:E.130, L:M.131, L:R.221, L:I.227, L:F.295, 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.9: 19 residues within 4Å: Chain M: M.89, G.92, Q.93, D.96, D.100, F.101, T.102 Chain N: R.127, E.130, M.131, T.217, F.220, R.221, G.223, H.224, I.227, F.295, L.305, N.309 16 PLIP interactions: 13 interactions with chain N, 3 interactions with chain M, Hydrophobic interactions: N:E.130, N:M.131, N:R.221, N:I.227, N:F.295, N:F.295, N:L.305, M:Q.93, M:D.96 Hydrogen bonds: N:N.309, M:T.102 Salt bridges: N:R.127, N:R.221, N:R.221, N:H.224 Metal complexes: N:H.224

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.5: 7 residues within 4Å: Chain L: N.77, S.79, N.80, L.84, A.86, V.87, Q.89 6 PLIP interactions: 6 interactions with chain L Hydrogen bonds: L:S.79, L:S.79, L:N.80, L:V.87, L:Q.89, L:Q.89 NAG.6: 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.10: 7 residues within 4Å: Chain N: N.77, N.80, L.82, L.84, A.86, V.87, Q.89 4 PLIP interactions: 4 interactions with chain N Hydrogen bonds: N:N.80, N:V.87, N:Q.89, N:Q.89 NAG.11: 5 residues within 4Å: Chain N: N.113, S.115, A.116, W.257, L.261 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.7: 5 residues within 4Å: Chain K: D.98 Chain L: T.56, F.58, D.60, S.62 5 PLIP interactions: 4 interactions with chain L, 1 interactions with chain K Metal complexes: L:T.56, L:T.56, L:F.58, L:D.60, K:D.98 CA.12: 5 residues within 4Å: Chain M: D.98 Chain N: T.56, F.58, D.60, S.62 5 PLIP interactions: 3 interactions with chain N, 2 interactions with chain M Metal complexes: N:T.56, N:T.56, N:F.58, M:D.98, M:D.98

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
M

M
K

L
N

N
L

Histone H3.2

Histone H4

Histone H2A type 1

Histone H2B 1.1

Myeloperoxidase light chain

Myeloperoxidase light chain

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