SMTL ID : 8ing.1

Structure of the ternary complex of lactoperoxidase with substrate nitric oxide (NO) and product nitrite ion (NO2) at 1.98 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 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: 3 residues within 4Å: Chain A: N.241, A.244, W.384 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.32 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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.205, A:S.208, A:V.215, A:Q.217, A:Q.217 NAG.4: 3 residues within 4Å: Chain A: N.332, S.334, V.335 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.332 Water bridges: A:N.332

2 x NO: NITRIC OXIDE(Non-covalent)

NO.5: 6 residues within 4Å: Chain A: Q.105, H.109, H.351 Ligands: NO2.6, IOD.18, HEM.27 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.105, A:H.351 Water bridges: A:R.255 NO.31: 5 residues within 4Å: Chain A: S.254, R.255, F.381 Ligands: NO2.6, NA.38 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.254

1 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.18, HEM.27, NO.31, NA.38 No protein-ligand interaction detected (PLIP)

7 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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.95, A:R.96, A:R.96, A:R.506, A:R.506 NO3.8: 5 residues within 4Å: Chain A: P.461, K.462, T.463, G.466 Ligands: IOD.26 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.462, A:T.463, A:G.466 NO3.13: 8 residues within 4Å: Chain A: E.363, Y.365, R.397, H.558, V.559, T.560, K.561 Ligands: IOD.25 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.363, A:R.397, A:T.560, A:K.561 NO3.14: 3 residues within 4Å: Chain A: P.197, S.198 Ligands: IOD.23 No protein-ligand interaction detected (PLIP) NO3.15: 6 residues within 4Å: Chain A: E.77, N.80, K.81, P.145, K.146 Ligands: IOD.24 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.80 NO3.16: 7 residues within 4Å: Chain A: V.215, N.216, Q.217, E.218, P.228, F.229 Ligands: IOD.22 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.216, A:Q.217, A:E.218, A:E.218, A:F.229 NO3.17: 3 residues within 4Å: Chain A: K.65, T.66 Ligands: SCN.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.65, A:T.66

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

SCN.9: 3 residues within 4Å: Chain A: T.66, N.68 Ligands: NO3.17 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.12: 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.32: 5 residues within 4Å: Chain A: H.565, A.566, F.567, Q.568 Ligands: NAG.2 No protein-ligand interaction detected (PLIP)

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

EDO.11: 5 residues within 4Å: Chain A: N.230, P.236, C.248, S.254, F.381 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.230 Water bridges: A:S.254 EDO.28: 7 residues within 4Å: Chain A: E.218, A.219, F.229, H.245, V.246, I.387, K.388 No protein-ligand interaction detected (PLIP) EDO.30: 2 residues within 4Å: Chain A: E.538, R.541 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.538, A:R.541

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

IOD.18: 7 residues within 4Å: Chain A: H.109, R.255, E.258 Ligands: NO.5, NO2.6, HEM.27, NA.38 Ligand excluded by PLIP IOD.19: 2 residues within 4Å: Chain A: P.236, T.425 Ligand excluded by PLIP IOD.20: 4 residues within 4Å: Chain A: Q.409, N.410, N.473, K.479 Ligand excluded by PLIP IOD.21: 5 residues within 4Å: Chain A: R.45, W.46, N.341, V.342, W.452 Ligand excluded by PLIP IOD.22: 4 residues within 4Å: Chain A: Q.217, E.218, F.229 Ligands: NO3.16 Ligand excluded by PLIP IOD.23: 3 residues within 4Å: Chain A: P.197, S.198 Ligands: NO3.14 Ligand excluded by PLIP IOD.24: 3 residues within 4Å: Chain A: N.80, P.145 Ligands: NO3.15 Ligand excluded by PLIP IOD.25: 5 residues within 4Å: Chain A: E.363, R.397, T.560, K.561 Ligands: NO3.13 Ligand excluded by PLIP IOD.26: 4 residues within 4Å: Chain A: K.462, T.463, G.466 Ligands: NO3.8 Ligand excluded by PLIP IOD.34: 2 residues within 4Å: Chain A: F.309, W.530 Ligand excluded by PLIP IOD.35: 3 residues within 4Å: Chain A: H.377 Ligands: IOD.36, IOD.37 Ligand excluded by PLIP IOD.36: 3 residues within 4Å: Chain A: H.377 Ligands: IOD.35, IOD.37 Ligand excluded by PLIP IOD.37: 4 residues within 4Å: Chain A: T.378, H.429 Ligands: IOD.35, IOD.36 Ligand excluded by PLIP

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.27: 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.18 26 PLIP interactions: 26 interactions with chain A, Hydrophobic interactions: A:Q.105, A:Q.105, A:E.258, 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:A.114, A:R.255, A:R.348, A:R.348, A:R.348, A:R.348 Salt bridges: A:R.255, A:R.348, A:R.440 Metal complexes: A:H.351

1 x CA: CALCIUM ION(Non-covalent)

CA.29: 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.33: 6 residues within 4Å: Chain A: L.224, A.225, R.271, R.275, R.278, N.556 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.225, A:R.275, A:R.278, A:N.556 Water bridges: A:R.278

2 x NA: SODIUM ION(Non-functional Binders)

NA.38: 4 residues within 4Å: Chain A: E.258 Ligands: NO2.6, IOD.18, NO.31 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.423 NA.39: 2 residues within 4Å: Chain A: S.198, R.202 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.202

Links

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Citation

Ahmad, M.I. et al., Structure of the ternary complex of lactoperoxidase with substrate nitric oxide (NO) and product nitrite ion (NO2) at 1.98 A resolution. To be published

Release Date

2023-04-05

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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