SMTL ID : 7wcs.1

Structure of the lactoperoxidase with bound nitric oxide and nitrite in the substrate binding site 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, OSM.14 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.208, A:V.215, A:Q.217, A:Q.217 Water bridges: A:N.205, A:N.205 NAG.4: 2 residues within 4Å: Chain A: N.332, S.334 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.332 Water bridges: A:S.334

1 x NO: NITRIC OXIDE(Non-covalent)

NO.5: 6 residues within 4Å: Chain A: Q.105, H.109, H.351 Ligands: NO2.6, IOD.24, HEM.37 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.105, A:H.351 Water bridges: A:R.255

1 x NO2: NITRITE ION(Non-covalent)

NO2.6: 8 residues within 4Å: Chain A: Q.105, H.109, R.255, E.258 Ligands: NO.5, IOD.24, NA.34, HEM.37 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.109

9 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: 4 residues within 4Å: Chain A: K.462, T.463, G.466 Ligands: IOD.33 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.462, A:T.463 NO3.10: 4 residues within 4Å: Chain A: R.31, R.32, N.333 Ligands: OSM.22 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.333 NO3.16: 4 residues within 4Å: Chain A: H.377, T.378, H.429 Ligands: NA.36 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.377 Water bridges: A:H.429 NO3.17: 8 residues within 4Å: Chain A: E.363, Y.365, R.397, H.558, V.559, T.560, K.561 Ligands: IOD.32 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.363, A:R.397, A:T.560, A:K.561 NO3.18: 3 residues within 4Å: Chain A: P.197, S.198 Ligands: IOD.30 No protein-ligand interaction detected (PLIP) NO3.19: 6 residues within 4Å: Chain A: E.77, N.80, K.81, P.145, K.146 Ligands: IOD.31 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.80 NO3.20: 7 residues within 4Å: Chain A: V.215, N.216, Q.217, E.218, P.228, F.229 Ligands: IOD.28 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.217, A:E.218, A:F.229 NO3.21: 2 residues within 4Å: Chain A: K.65, T.66 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: F.59, T.66, N.68 No protein-ligand interaction detected (PLIP) SCN.11: 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.13: 4 residues within 4Å: Chain A: R.76, P.149, K.150, N.419 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.150 SCN.15: 5 residues within 4Å: Chain A: L.224, A.225, R.271, R.275, R.278 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.275, A:R.278

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

EDO.12: 5 residues within 4Å: Chain A: N.230, P.236, C.248, S.254, F.381 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.230 Water bridges: A:S.254, A:S.257 EDO.23: 6 residues within 4Å: Chain A: I.306, F.309, R.310, W.529, W.530 Ligands: IOD.29 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.530 EDO.38: 6 residues within 4Å: Chain A: E.218, A.219, F.229, H.245, V.246, I.387 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.245 EDO.40: 2 residues within 4Å: Chain A: E.538, R.541 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.541

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

OSM.14: 6 residues within 4Å: Chain A: D.311, H.565, A.566, F.567, Q.568 Ligands: NAG.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.566, A:F.567 OSM.22: 5 residues within 4Å: Chain A: R.31, Y.331, N.333, R.527 Ligands: NO3.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.31

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

IOD.24: 7 residues within 4Å: Chain A: H.109, R.255, E.258 Ligands: NO.5, NO2.6, NA.34, HEM.37 Ligand excluded by PLIP IOD.25: 2 residues within 4Å: Chain A: P.236, T.425 Ligand excluded by PLIP IOD.26: 4 residues within 4Å: Chain A: Q.409, N.410, N.473, K.479 Ligand excluded by PLIP IOD.27: 6 residues within 4Å: Chain A: A.44, R.45, W.46, N.341, V.342, W.452 Ligand excluded by PLIP IOD.28: 3 residues within 4Å: Chain A: Q.217, F.229 Ligands: NO3.20 Ligand excluded by PLIP IOD.29: 3 residues within 4Å: Chain A: F.309, W.530 Ligands: EDO.23 Ligand excluded by PLIP IOD.30: 3 residues within 4Å: Chain A: P.197, S.198 Ligands: NO3.18 Ligand excluded by PLIP IOD.31: 3 residues within 4Å: Chain A: N.80, P.145 Ligands: NO3.19 Ligand excluded by PLIP IOD.32: 5 residues within 4Å: Chain A: E.363, R.397, T.560, K.561 Ligands: NO3.17 Ligand excluded by PLIP IOD.33: 4 residues within 4Å: Chain A: K.462, T.463, G.466 Ligands: NO3.8 Ligand excluded by PLIP

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

NA.34: 4 residues within 4Å: Chain A: E.258, F.381 Ligands: NO2.6, IOD.24 No protein-ligand interaction detected (PLIP) NA.35: 2 residues within 4Å: Chain A: S.198, R.202 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.202 NA.36: 2 residues within 4Å: Chain A: H.429 Ligands: NO3.16 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.429

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.37: 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.24 27 PLIP interactions: 27 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:F.113, A:R.255, 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.39: 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

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Viswanathan, V. et al., Structure of the lactoperoxidase with bound nitric oxide and nitrite in the substrate binding site at 1.98 A resolution. To Be Published

Release Date

2022-02-09

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

Related Entries With Identical Sequence