SMTL ID : 7vin.1

Structure of the complex of lactoperoxidase with nitric oxide catalytic product nitrite at 1.89 A resolution.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 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: 6 residues within 4Å: Chain A: N.205, S.208, A.214, V.215, Q.217, W.220 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.217 Water bridges: A:Q.217

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

NAG.2: 3 residues within 4Å: Chain A: N.95, R.96, I.315 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.96 Water bridges: A:N.95 NAG.3: 4 residues within 4Å: Chain A: N.241, A.244, W.384, K.388 No protein-ligand interaction detected (PLIP) NAG.4: 2 residues within 4Å: Chain A: N.332, V.335 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.332 Water bridges: A:N.332, A:D.336

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 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

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

IOD.6: 2 residues within 4Å: Chain A: N.80, P.145 Ligand excluded by PLIP IOD.7: 1 residues within 4Å: Chain A: W.530 Ligand excluded by PLIP IOD.8: 1 residues within 4Å: Chain A: R.31 Ligand excluded by PLIP IOD.9: 2 residues within 4Å: Chain A: S.359, K.402 Ligand excluded by PLIP IOD.10: 1 residues within 4Å: Chain A: G.466 Ligand excluded by PLIP IOD.11: 2 residues within 4Å: Chain A: P.375, K.420 Ligand excluded by PLIP IOD.12: 3 residues within 4Å: Chain A: E.218, F.229, N.231 Ligand excluded by PLIP IOD.13: 2 residues within 4Å: Chain A: P.236, T.425 Ligand excluded by PLIP IOD.14: 3 residues within 4Å: Chain A: R.76, P.149, N.419 Ligand excluded by PLIP IOD.23: 5 residues within 4Å: Chain A: H.109, R.255, E.258 Ligands: NO2.18, HEM.20 Ligand excluded by PLIP IOD.24: 1 residues within 4Å: Chain A: S.198 Ligand excluded by PLIP IOD.25: 4 residues within 4Å: Chain A: K.150, N.419, H.429, G.430 Ligand excluded by PLIP IOD.26: 1 residues within 4Å: Chain A: R.202 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: S.33, P.34, A.35 Ligand excluded by PLIP IOD.29: 2 residues within 4Å: Chain A: L.86, D.87 Ligand excluded by PLIP IOD.30: 2 residues within 4Å: Chain A: H.222, H.558 Ligand excluded by PLIP IOD.31: 5 residues within 4Å: Chain A: E.363, Y.365, I.559, T.560, K.561 Ligand excluded by PLIP IOD.32: 1 residues within 4Å: Chain A: R.506 Ligand excluded by PLIP IOD.33: 4 residues within 4Å: Chain A: C.15, E.17, C.28, R.31 Ligand excluded by PLIP IOD.34: 3 residues within 4Å: Chain A: H.377, H.429 Ligands: SCN.22 Ligand excluded by PLIP IOD.35: 4 residues within 4Å: Chain A: D.311, H.565, A.566, F.567 Ligand excluded by PLIP

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

SCN.15: 4 residues within 4Å: Chain A: N.230, P.236, C.248, F.381 No protein-ligand interaction detected (PLIP) SCN.21: 3 residues within 4Å: Chain A: I.24, P.197 Ligands: EDO.19 No protein-ligand interaction detected (PLIP) SCN.22: 3 residues within 4Å: Chain A: H.377, T.378 Ligands: IOD.34 No protein-ligand interaction detected (PLIP)

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

EDO.16: 5 residues within 4Å: Chain A: L.224, A.225, R.271, N.274, R.278 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.274, A:R.278, A:R.278 EDO.17: 4 residues within 4Å: Chain A: N.450, S.451, Q.460, D.488 4 PLIP interactions: 4 interactions with chain A Water bridges: A:N.68, A:S.451, A:S.451, A:D.488 EDO.19: 5 residues within 4Å: Chain A: T.23, I.24, T.25, P.197 Ligands: SCN.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.24, A:T.25

1 x NO2: NITRITE ION(Non-covalent)

NO2.18: 5 residues within 4Å: Chain A: Q.105, H.109, R.255 Ligands: HEM.20, IOD.23 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.105 Water bridges: A:R.255

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.20: 22 residues within 4Å: Chain A: M.101, G.104, Q.105, D.108, H.109, D.112, R.255, E.258, Q.259, T.344, F.347, R.348, G.350, H.351, V.354, F.380, L.417, L.433, I.436, R.440 Ligands: NO2.18, IOD.23 24 PLIP interactions: 24 interactions with chain A, Hydrophobic interactions: 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 Water bridges: A:E.116, A:E.116, A:R.255, A:R.348, A:Q.423, A:R.440 Salt bridges: A:H.109, A:R.255, A:R.348, A:R.440 Metal complexes: A:H.351

1 x ZN: ZINC ION(Non-covalent)

ZN.36: 3 residues within 4Å: Chain A: E.130, H.426, K.427 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.130, H2O.1, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Viswanathan, V. et al., Structure of the complex of lactoperoxidase with nitric oxide catalytic product nitrite at 1.89 A resolution. To Be Published

Release Date

2021-10-20

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

Related Entries With Identical Sequence