SMTL ID : 8ogi.1

Structure of native human eosinophil peroxidase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 11 residues within 4Å: Chain B: N.77, R.78, T.79, N.80, L.82, L.84, A.86, I.87, N.88, Q.89, Q.92 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.89 Water bridges: B:Q.89, B:Q.92

1 x HEB: HEME B/C(Covalent)

HEB.2: 34 residues within 4Å: Chain A: M.86, Q.87, G.89, Q.90, D.93, D.97, F.98, S.99 Chain B: R.127, E.130, T.131, K.133, F.184, T.217, F.220, R.221, F.222, G.223, H.224, M.226, L.227, L.249, F.253, L.290, L.294, F.295, L.305, L.308, N.309, R.312 Ligands: EDO.8, EDO.20, FLC.21, ACT.22 20 PLIP interactions: 4 interactions with chain A, 15 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: A:Q.90, A:Q.90, B:E.130, B:T.131, B:R.221, B:L.227, B:F.253, B:F.295, B:L.305, B:L.305, B:L.308 Hydrogen bonds: A:D.97, A:S.99 Water bridges: B:T.217, B:R.221 Salt bridges: B:R.127, B:R.221, B:R.312 Metal complexes: B:H.224, H2O.2

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: T.10, R.12, L.20, A.23, S.24, N.25, Q.26 Ligands: FLC.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.10, A:T.10, A:N.25, A:Q.26 GOL.5: 4 residues within 4Å: Chain A: E.35, F.44, R.52, N.53 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.52, A:R.52, A:N.53, A:N.53 Water bridges: A:N.53 GOL.11: 6 residues within 4Å: Chain B: Q.282, D.283, N.345, D.347, L.348, K.351 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.345, B:K.351 Water bridges: B:D.347, A:I.67 GOL.15: 14 residues within 4Å: Chain B: D.102, L.104, P.108, C.109, C.120, F.121, L.122, A.123, T.126, R.127, S.128, T.129, E.130, F.254 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:F.121, B:F.121, B:F.121, B:S.128, B:T.129 Water bridges: B:S.128, B:S.128 GOL.18: 7 residues within 4Å: Chain B: R.74, L.75, A.86, P.100, F.101, L.122 Ligands: ACT.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.74, B:R.74 GOL.19: 4 residues within 4Å: Chain B: S.70, L.73, R.74, R.78 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.78, B:R.78

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 8 residues within 4Å: Chain A: F.70, P.71, N.72, L.75 Chain B: P.229, V.287, D.288 Ligands: CL.14 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.288, B:D.288 Water bridges: A:F.70, A:N.72 EDO.8: 11 residues within 4Å: Chain A: F.98, S.99, P.100, E.101 Chain B: S.37, A.38, R.312 Ligands: HEB.2, EDO.20, FLC.21, ACT.22 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.37, A:E.101 EDO.16: 5 residues within 4Å: Chain A: D.4, K.16 Chain B: Y.204, R.399, K.404 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.399, B:K.404 Water bridges: B:R.399 EDO.17: 6 residues within 4Å: Chain B: G.190, K.191, A.192, R.193, P.375, G.376 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.191, B:A.192 Water bridges: B:G.190, B:R.193 EDO.20: 11 residues within 4Å: Chain A: F.98, S.99 Chain B: S.37, R.127, T.217, R.221, R.312, H.316 Ligands: HEB.2, EDO.8, FLC.21 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.221 Water bridges: B:R.127, A:S.99

3 x FLC: CITRATE ANION(Non-covalent)

FLC.6: 6 residues within 4Å: Chain A: T.8, I.9, T.10, R.12 Chain B: V.69 Ligands: FLC.12 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:I.9 Water bridges: A:T.10, A:R.12, A:R.12 Hydrophobic interactions: B:V.69 FLC.12: 7 residues within 4Å: Chain A: T.10, N.25 Chain B: E.68, V.69, S.70 Ligands: GOL.3, FLC.6 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.69 Hydrogen bonds: B:E.68, B:E.68, B:E.68, B:V.69, B:S.70, B:S.70 FLC.21: 11 residues within 4Å: Chain A: F.98, E.101 Chain B: R.127, E.130, F.254, F.295, R.299 Ligands: HEB.2, EDO.8, EDO.20, ACT.22 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.295 Water bridges: B:R.299, B:R.299 Salt bridges: B:R.299

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

CL.7: 9 residues within 4Å: Chain A: A.29, R.30, W.31, L.32 Chain B: A.213, N.214, V.215, L.318, W.324 Ligand excluded by PLIP CL.14: 6 residues within 4Å: Chain B: P.229, V.287, D.288, E.289, R.293 Ligands: EDO.4 Ligand excluded by PLIP

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

NAG.9: 5 residues within 4Å: Chain B: N.113, S.115, A.116, W.257, Y.261 No protein-ligand interaction detected (PLIP)

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.10: 7 residues within 4Å: Chain B: I.87, N.88, Q.89, R.90, P.100, F.101 Ligands: GOL.18 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.101 Hydrogen bonds: B:Q.89, B:F.101 ACT.22: 10 residues within 4Å: Chain A: E.101 Chain B: L.294, F.295, R.299, L.303, L.308, R.312 Ligands: HEB.2, EDO.8, FLC.21 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.303 Water bridges: B:R.312 Salt bridges: B:R.312

1 x CA: CALCIUM ION(Non-covalent)

CA.13: 6 residues within 4Å: Chain A: D.95, L.96 Chain B: T.56, F.58, D.60, S.62 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Metal complexes: B:T.56, B:F.58, B:D.60, B:S.62, A:D.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pfanzagl, V. et al., Posttranslational modification and heme cavity architecture of human eosinophil peroxidase-insights from first crystal structure and biochemical characterization. J.Biol.Chem. (2023)

Release Date

2024-01-24

Peptides

Eosinophil peroxidase light chain: A
Eosinophil peroxidase heavy chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Eosinophil peroxidase light chain

Eosinophil peroxidase heavy chain