SMTL ID : 9ku6.1

Crystal structure of the complex of lactoperoxidase with nitric oxide at 1.72 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 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: 5 residues within 4Å: Chain A: N.241, A.244, W.384, R.385, K.388 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.385

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

NAG.2: 3 residues within 4Å: Chain A: N.332, S.334, V.335 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.332, A:N.332, A:N.332 NAG.16: 5 residues within 4Å: Chain A: N.205, S.208, 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.39: 5 residues within 4Å: Chain A: N.95, R.96, I.315, Q.568 Ligands: SCN.25 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.95, A:R.96, A:R.96, A:Q.568

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

IOD.3: 7 residues within 4Å: Chain A: A.44, R.45, W.46, N.341, V.342, W.452 Ligands: SCN.22 Ligand excluded by PLIP IOD.4: 2 residues within 4Å: Chain A: N.80, P.145 Ligand excluded by PLIP IOD.5: 4 residues within 4Å: Chain A: N.216, Q.217, F.229 Ligands: SCN.20 Ligand excluded by PLIP IOD.6: 3 residues within 4Å: Chain A: F.309, W.530 Ligands: SCN.32 Ligand excluded by PLIP IOD.7: 1 residues within 4Å: Ligands: SCN.26 Ligand excluded by PLIP IOD.8: 2 residues within 4Å: Chain A: L.224, A.225 Ligand excluded by PLIP IOD.9: 3 residues within 4Å: Chain A: S.359, E.373 Ligands: SCN.29 Ligand excluded by PLIP IOD.10: 1 residues within 4Å: Chain A: P.197 Ligand excluded by PLIP IOD.11: 2 residues within 4Å: Chain A: L.86, D.87 Ligand excluded by PLIP IOD.12: 3 residues within 4Å: Chain A: R.202 Ligands: IOD.44, IOD.46 Ligand excluded by PLIP IOD.13: 2 residues within 4Å: Chain A: S.198 Ligands: SCN.30 Ligand excluded by PLIP IOD.14: 3 residues within 4Å: Chain A: P.236, T.425 Ligands: SCN.21 Ligand excluded by PLIP IOD.15: 2 residues within 4Å: Chain A: T.66 Ligands: SCN.31 Ligand excluded by PLIP IOD.42: 6 residues within 4Å: Chain A: R.255, E.258 Ligands: NO2.35, NO.36, HEM.40, IOD.48 Ligand excluded by PLIP IOD.43: 3 residues within 4Å: Chain A: F.381 Ligands: IOD.48, IOD.51 Ligand excluded by PLIP IOD.44: 3 residues within 4Å: Chain A: S.198 Ligands: IOD.12, IOD.46 Ligand excluded by PLIP IOD.45: 3 residues within 4Å: Chain A: A.35, R.41, R.338 Ligand excluded by PLIP IOD.46: 2 residues within 4Å: Ligands: IOD.12, IOD.44 Ligand excluded by PLIP IOD.47: 2 residues within 4Å: Chain A: H.377 Ligands: SCN.18 Ligand excluded by PLIP IOD.48: 4 residues within 4Å: Chain A: E.258 Ligands: NO2.35, IOD.42, IOD.43 Ligand excluded by PLIP IOD.49: 6 residues within 4Å: Chain A: E.363, R.397, I.559, T.560, K.561 Ligands: SCN.23 Ligand excluded by PLIP IOD.50: 3 residues within 4Å: Chain A: K.462, T.463 Ligands: SCN.17 Ligand excluded by PLIP IOD.51: 4 residues within 4Å: Chain A: P.236 Ligands: NO.37, NO2.38, IOD.43 Ligand excluded by PLIP IOD.52: 6 residues within 4Å: Chain A: N.230, K.232, S.235, P.247, C.248 Ligands: NO2.38 Ligand excluded by PLIP

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

SCN.17: 4 residues within 4Å: Chain A: K.462, T.463, G.466 Ligands: IOD.50 Ligand excluded by PLIP SCN.18: 4 residues within 4Å: Chain A: H.377, T.378, H.429 Ligands: IOD.47 Ligand excluded by PLIP SCN.19: 4 residues within 4Å: Chain A: H.565, A.566, F.567, Q.568 Ligand excluded by PLIP SCN.20: 5 residues within 4Å: Chain A: E.218, P.228, F.229, N.231 Ligands: IOD.5 Ligand excluded by PLIP SCN.21: 5 residues within 4Å: Chain A: P.234, S.235, P.236, T.425 Ligands: IOD.14 Ligand excluded by PLIP SCN.22: 10 residues within 4Å: Chain A: A.44, R.45, W.46, L.47, S.340, N.341, V.342, M.446, W.452 Ligands: IOD.3 Ligand excluded by PLIP SCN.23: 8 residues within 4Å: Chain A: E.363, Y.365, R.397, H.558, I.559, T.560, K.561 Ligands: IOD.49 Ligand excluded by PLIP SCN.24: 4 residues within 4Å: Chain A: R.76, P.149, K.150, N.419 Ligand excluded by PLIP SCN.25: 4 residues within 4Å: Chain A: N.95, R.96, R.506 Ligands: NAG.39 Ligand excluded by PLIP SCN.26: 4 residues within 4Å: Chain A: F.229, R.245, I.387 Ligands: IOD.7 Ligand excluded by PLIP SCN.27: 4 residues within 4Å: Chain A: R.45, W.46, L.47, P.48 Ligand excluded by PLIP SCN.28: 5 residues within 4Å: Chain A: D.410, N.473, I.475, L.476, K.479 Ligand excluded by PLIP SCN.29: 5 residues within 4Å: Chain A: S.359, L.361, P.367, K.402 Ligands: IOD.9 Ligand excluded by PLIP SCN.30: 4 residues within 4Å: Chain A: E.196, P.197, S.198 Ligands: IOD.13 Ligand excluded by PLIP SCN.31: 3 residues within 4Å: Chain A: K.65, T.66 Ligands: IOD.15 Ligand excluded by PLIP SCN.32: 4 residues within 4Å: Chain A: I.306, F.309, W.530 Ligands: IOD.6 Ligand excluded by PLIP SCN.34: 3 residues within 4Å: Chain A: R.31, R.32, N.333 Ligand excluded by PLIP

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.33: 8 residues within 4Å: Chain A: N.30, R.32, S.33, L.36, N.333, S.334, D.336, R.338 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.30 Water bridges: A:S.33, A:S.33

2 x NO2: NITRITE ION(Non-covalent)

NO2.35: 8 residues within 4Å: Chain A: Q.105, H.109, R.255, E.258 Ligands: NO.36, HEM.40, IOD.42, IOD.48 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.255, A:R.255 NO2.38: 7 residues within 4Å: Chain A: N.230, K.232, P.236, C.248 Ligands: NO.37, IOD.51, IOD.52 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.232 Water bridges: A:N.230, A:F.254

2 x NO: NITRIC OXIDE(Non-covalent)

NO.36: 6 residues within 4Å: Chain A: Q.105, H.109, H.351 Ligands: NO2.35, HEM.40, IOD.42 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.105, A:H.109 Water bridges: A:R.255 NO.37: 8 residues within 4Å: Chain A: C.248, F.254, R.255, A.256, S.257, F.381 Ligands: NO2.38, IOD.51 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.254, A:S.257 Water bridges: A:F.249, A:A.256

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.40: 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: NO2.35, NO.36, IOD.42 28 PLIP interactions: 27 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Q.105, A:Q.105, A:E.258, A:Q.259, A:F.347, 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:D.112, A:A.114 Water bridges: A:R.255, A:R.348, A:R.348, A:R.348, A:R.348 Salt bridges: A:R.348, A:R.348, A:R.440 Metal complexes: A:H.351, NO.36

1 x CA: CALCIUM ION(Non-covalent)

CA.41: 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

Links

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Citation

Maurya, A. et al., Crystal structure of the complex of lactoperoxidase with nitric oxide at 1.72 A resolution. To Be Published

Release Date

2024-12-18

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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