SMTL ID : 9ger.1

Native dimeric Myeloperoxidase bound to nucleosome core particle, intermediate state; 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: 8 residues within 4Å: Chain B: R.202, N.205, R.392 Chain D: F.327, C.328, T.389 Ligands: NAG-NAG-BMA-MAN-MAN-FUC.2, NAG-NAG-BMA-MAN-MAN-FUC.2 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-FUC.2: 9 residues within 4Å: Chain A: W.34 Chain B: F.327, C.328, G.329, K.393 Chain D: N.205, V.208 Ligands: NAG-NAG-BMA-MAN-MAN-FUC.1, NAG-NAG-BMA-MAN-MAN-FUC.1 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: B:C.328, B:K.393, A:W.34 Hydrophobic interactions: D:V.208

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

CL.3: 5 residues within 4Å: Chain A: V.32, R.33, W.34, L.35 Chain B: V.215 Ligand excluded by PLIP

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.4: 9 residues within 4Å: Chain A: G.92, Q.93, D.96 Chain B: R.127, E.130, M.131, F.220, R.221, H.224 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:M.131, A:D.96 Hydrogen bonds: B:R.127, B:R.221 Salt bridges: B:R.127 Metal complexes: B:H.224 HEM.8: 14 residues within 4Å: Chain C: M.89, G.92, Q.93, D.96, T.102 Chain D: R.127, E.130, M.131, F.220, R.221, G.223, H.224, I.227, L.305 10 PLIP interactions: 7 interactions with chain D, 3 interactions with chain C, Hydrophobic interactions: D:F.220, D:I.227, D:L.305, C:Q.93, C:D.96 Salt bridges: D:R.127, D:R.221 pi-Stacking: D:H.224 Metal complexes: D:H.224 Hydrogen bonds: C:T.102

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

NAG.5: 2 residues within 4Å: Chain B: N.77, V.87 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.77, B:N.77, B:V.87 NAG.6: 4 residues within 4Å: Chain B: N.113, S.115, W.257, L.261 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.113 NAG.9: 5 residues within 4Å: Chain D: N.77, N.80, L.84, A.86, V.87 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:N.77, D:A.86 Hydrogen bonds: D:N.77, D:N.80, D:V.87 NAG.10: 4 residues within 4Å: Chain D: N.113, A.116, W.257, L.261 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.113

1 x CA: CALCIUM ION(Non-covalent)

CA.7: 5 residues within 4Å: Chain A: D.98 Chain B: T.56, F.58, D.60, S.62 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:T.56, B:T.56, B:F.58, B:D.60, B:S.62

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

Myeloperoxidase light chain: AC
Myeloperoxidase light chain: BD
Histone H3.2: EI
Histone H4: FJ
Histone H2A type 1: GK
Histone H2B 1.1: HL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
K

C
M

B
L

D
N

E
A

I
E

F
B

J
F

G
C

K
G

H
D

L
H

Myeloperoxidase light chain

Myeloperoxidase light chain

Histone H3.2

Histone H4

Histone H2A type 1

Histone H2B 1.1

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