SMTL ID : 8y9x.1

Crystal structure of the complex of lactoperoxidase with four inorganic substrates, SCN, I, Br and Cl

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.1: 23 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: BR.11 26 PLIP interactions: 25 interactions with chain A, 1 Ligand-Water 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:A.114 Water bridges: A:R.255, A:R.255, A:R.348, A:R.348 Salt bridges: A:R.255, A:R.348, A:R.440 Metal complexes: A:H.351, H2O.4

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 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

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

IOD.3: 2 residues within 4Å: Chain A: N.80, P.145 Ligand excluded by PLIP IOD.4: 2 residues within 4Å: Chain A: P.236, P.424 Ligand excluded by PLIP IOD.5: 3 residues within 4Å: Chain A: N.216, Q.217, F.229 Ligand excluded by PLIP IOD.6: 2 residues within 4Å: Chain A: F.309, W.530 Ligand excluded by PLIP IOD.7: 4 residues within 4Å: Chain A: E.363, R.397, I.559, T.560 Ligand excluded by PLIP IOD.8: 3 residues within 4Å: Chain A: N.95, R.96, R.506 Ligand excluded by PLIP IOD.9: 3 residues within 4Å: Chain A: K.462, G.466 Ligands: PEG.19 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain A: L.224, A.225 Ligand excluded by PLIP IOD.13: 2 residues within 4Å: Chain A: S.198, R.202 Ligand excluded by PLIP IOD.32: 7 residues within 4Å: Chain A: A.44, R.45, W.46, L.47, N.341, V.342, W.452 Ligand excluded by PLIP IOD.33: 2 residues within 4Å: Chain A: E.196, S.198 Ligand excluded by PLIP

1 x BR: BROMIDE ION(Non-covalent)

BR.11: 4 residues within 4Å: Chain A: R.255, E.258 Ligands: HEM.1, CL.12 Ligand excluded by PLIP

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.12: 3 residues within 4Å: Chain A: E.258, F.381 Ligands: BR.11 Ligand excluded by PLIP

7 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.14: 6 residues within 4Å: Chain A: R.76, N.80, P.149, K.150, R.418, N.419 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.76, A:N.80, A:K.150, A:K.150, A:R.418, A:R.418, A:N.419 PEG.15: 4 residues within 4Å: Chain A: R.32, L.36, N.333, S.334 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.32, A:R.32, A:N.333 PEG.16: 3 residues within 4Å: Chain A: R.245, I.387, K.388 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.245, A:K.388 PEG.17: 5 residues within 4Å: Chain A: N.216, Q.217, A.219, W.220, A.225 No protein-ligand interaction detected (PLIP) PEG.18: 4 residues within 4Å: Chain A: P.197, S.201, L.206 Ligands: SCN.21 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.204 PEG.19: 5 residues within 4Å: Chain A: S.459, P.461, T.469, V.470 Ligands: IOD.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.459 Water bridges: A:S.459 PEG.20: 3 residues within 4Å: Chain A: K.472, P.500, M.501 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.472

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

SCN.21: 3 residues within 4Å: Chain A: T.23, I.24 Ligands: PEG.18 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.24 SCN.22: 3 residues within 4Å: Chain A: R.453, L.458, P.509 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.453 SCN.23: 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.24: 2 residues within 4Å: Chain A: H.377, H.429 No protein-ligand interaction detected (PLIP) SCN.31: 5 residues within 4Å: Chain A: N.230, K.232, P.234, P.236, C.248 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.232

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)(Non-functional Binders)

NAG.25: 4 residues within 4Å: Chain A: N.95, R.96, I.315, Q.568 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.96 NAG.26: 5 residues within 4Å: Chain A: N.241, A.244, W.384, K.388 Ligands: NAG.27 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.241, A:A.244 NAG.27: 2 residues within 4Å: Chain A: E.371 Ligands: NAG.26 No protein-ligand interaction detected (PLIP) NAG.28: 3 residues within 4Å: Chain A: N.332, S.334, V.335 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.332 Water bridges: A:S.334, A:D.336 NAG.29: 7 residues within 4Å: Chain A: N.205, S.208, L.210, A.214, V.215, Q.217 Ligands: NAG.30 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.30: 1 residues within 4Å: Ligands: NAG.29 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Viswanathan, V. et al., Structural evidence for the order of preference of inorganic substrates in mammalian heme peroxidases: crystal structure of the complex of lactoperoxidase with four inorganic substrates, SCN, I, Br and Cl. To Be Published

Release Date

2024-03-13

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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