SMTL ID : 9it8.1

Crystal structure of the ternary complex of lactoperoxidase with nitric oxide and nitrite ion at 1.95 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

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: 4 residues within 4Å: Chain A: N.241, A.244, W.384, K.388 No protein-ligand interaction detected (PLIP)

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

NAG.2: 6 residues within 4Å: Chain A: N.95, R.96, I.315, Q.568 Ligands: NO3.7, SCN.28 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.96 NAG.3: 6 residues within 4Å: Chain A: N.205, S.208, L.210, A.214, V.215, Q.217 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Q.217 Hydrogen bonds: A:S.208, A:V.215, A:Q.217, A:Q.217 Water bridges: A:N.205, A:N.205 NAG.4: 3 residues within 4Å: Chain A: N.332, S.334, V.335 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.332

2 x NO: NITRIC OXIDE(Non-covalent)

NO.5: 5 residues within 4Å: Chain A: Q.105, H.109 Ligands: NO2.6, IOD.17, HEM.25 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.105 Water bridges: A:R.255 NO.35: 8 residues within 4Å: Chain A: C.248, F.254, R.255, A.256, S.257, E.258, F.381 Ligands: NO2.36 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.255, A:S.257, A:E.258 Water bridges: A:A.256, A:A.256

2 x NO2: NITRITE ION(Non-covalent)

NO2.6: 9 residues within 4Å: Chain A: Q.105, H.109, R.255, E.258 Ligands: NO.5, IOD.17, HEM.25, IOD.42, IOD.43 No protein-ligand interaction detected (PLIP) NO2.36: 4 residues within 4Å: Chain A: N.230, P.236, C.248 Ligands: NO.35 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.230

8 x NO3: NITRATE ION(Non-functional Binders)

NO3.7: 5 residues within 4Å: Chain A: N.95, R.96, R.504, R.506 Ligands: NAG.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.95, A:R.96, A:R.96, A:R.504, A:R.506, A:R.506 NO3.8: 4 residues within 4Å: Chain A: K.462, T.463, G.466 Ligands: IOD.24 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.462, A:T.463 NO3.12: 8 residues within 4Å: Chain A: E.363, Y.365, R.397, H.558, I.559, T.560, K.561 Ligands: IOD.23 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.363, A:R.397, A:H.558, A:T.560, A:K.561 NO3.13: 4 residues within 4Å: Chain A: E.196, P.197, S.198 Ligands: IOD.21 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.198 NO3.14: 6 residues within 4Å: Chain A: E.77, N.80, K.81, P.145, K.146 Ligands: IOD.22 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.80 NO3.15: 6 residues within 4Å: Chain A: N.216, Q.217, E.218, F.229, N.231 Ligands: IOD.20 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.216, A:Q.217, A:E.218, A:F.229 NO3.16: 2 residues within 4Å: Chain A: K.65, T.66 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.66 NO3.34: 5 residues within 4Å: Chain A: I.306, F.309, W.529, W.530 Ligands: IOD.30 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.530

6 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.9: 3 residues within 4Å: Chain A: T.66, R.67, N.68 No protein-ligand interaction detected (PLIP) SCN.10: 4 residues within 4Å: Chain A: S.359, L.361, P.367, K.402 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.402 SCN.11: 4 residues within 4Å: Chain A: R.76, P.149, K.150, N.419 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.150 Water bridges: A:T.153 SCN.28: 4 residues within 4Å: Chain A: H.565, A.566, F.567 Ligands: NAG.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.568 SCN.37: 2 residues within 4Å: Chain A: P.197, A.200 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.204 SCN.38: 6 residues within 4Å: Chain A: Q.409, D.410, N.473, I.475, L.476, K.479 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.479

17 x IOD: IODIDE ION(Non-functional Binders)

IOD.17: 6 residues within 4Å: Chain A: R.255, E.258 Ligands: NO.5, NO2.6, HEM.25, IOD.42 Ligand excluded by PLIP IOD.18: 2 residues within 4Å: Chain A: P.236, T.425 Ligand excluded by PLIP IOD.19: 6 residues within 4Å: Chain A: A.44, R.45, W.46, N.341, V.342, W.452 Ligand excluded by PLIP IOD.20: 4 residues within 4Å: Chain A: N.216, Q.217, F.229 Ligands: NO3.15 Ligand excluded by PLIP IOD.21: 3 residues within 4Å: Chain A: P.197, S.198 Ligands: NO3.13 Ligand excluded by PLIP IOD.22: 3 residues within 4Å: Chain A: N.80, P.145 Ligands: NO3.14 Ligand excluded by PLIP IOD.23: 5 residues within 4Å: Chain A: R.397, I.559, T.560, K.561 Ligands: NO3.12 Ligand excluded by PLIP IOD.24: 4 residues within 4Å: Chain A: K.462, T.463, G.466 Ligands: NO3.8 Ligand excluded by PLIP IOD.30: 3 residues within 4Å: Chain A: F.309, W.530 Ligands: NO3.34 Ligand excluded by PLIP IOD.31: 4 residues within 4Å: Chain A: H.377, H.429 Ligands: IOD.32, IOD.33 Ligand excluded by PLIP IOD.32: 4 residues within 4Å: Chain A: H.377, H.429 Ligands: IOD.31, IOD.33 Ligand excluded by PLIP IOD.33: 4 residues within 4Å: Chain A: T.378, H.429 Ligands: IOD.31, IOD.32 Ligand excluded by PLIP IOD.39: 4 residues within 4Å: Chain A: S.198, R.202 Ligands: IOD.40, IOD.41 Ligand excluded by PLIP IOD.40: 3 residues within 4Å: Chain A: S.198 Ligands: IOD.39, IOD.41 Ligand excluded by PLIP IOD.41: 2 residues within 4Å: Ligands: IOD.39, IOD.40 Ligand excluded by PLIP IOD.42: 4 residues within 4Å: Chain A: E.258 Ligands: NO2.6, IOD.17, IOD.43 Ligand excluded by PLIP IOD.43: 4 residues within 4Å: Chain A: F.254, F.381 Ligands: NO2.6, IOD.42 Ligand excluded by PLIP

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.25: 25 residues within 4Å: Chain A: M.101, G.104, Q.105, D.108, D.112, F.113, A.114, R.255, E.258, Q.259, T.344, F.347, R.348, G.350, H.351, V.354, F.380, L.417, Q.423, L.433, I.436, R.440 Ligands: NO.5, NO2.6, IOD.17 24 PLIP interactions: 24 interactions with chain A, Hydrophobic interactions: A:Q.105, A:Q.105, A:Q.259, A:F.347, A:F.347, A:R.348, A:V.354, A:V.354, A:F.380, A:L.417, A:L.433, A:L.433, A:I.436 Hydrogen bonds: A:D.112, A:A.114 Water bridges: A:F.113, A:A.114, A:R.255, A:R.348, A:R.348 Salt bridges: A:R.348, A:R.348, A:R.440 Metal complexes: A:H.351

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

EDO.26: 6 residues within 4Å: Chain A: A.219, F.229, R.245, V.246, P.247, I.387 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.27: 5 residues within 4Å: Chain A: D.110, T.184, F.186, D.188, S.190 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.110, A:D.110, A:T.184, A:F.186, A:S.190

1 x OSM: 1-(OXIDOSULFANYL)METHANAMINE(Non-covalent)

OSM.29: 4 residues within 4Å: Chain A: A.225, R.271, R.278, N.556 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.225, A:R.278, A:N.556 Water bridges: A:R.278

Links

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Citation

Maurya, A. et al., Crystal structure of the ternary complex of lactoperoxidase with nitric oxide and nitrite ion at 1.95 A resolution. To Be Published

Release Date

2024-09-11

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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