SMTL ID : 7de5.1

Crystal structure of yak lactoperoxidase at 1.55 A resolution.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN.1: 6 residues within 4Å: Chain A: N.205, S.208, A.214, V.215, Q.217 Ligands: IOD.34 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.217 Water bridges: A:Q.217, A:W.220

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.2: 4 residues within 4Å: Chain A: N.241, A.244, W.384, K.388 No protein-ligand interaction detected (PLIP)

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.3: 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, L.376, F.380, L.417, Q.423, L.433, I.436, R.440 Ligands: IOD.45, IOD.46 28 PLIP interactions: 27 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:L.376, 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.440 Metal complexes: A:H.351, H2O.6

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

NAG.4: 4 residues within 4Å: Chain A: N.95, R.96, I.315 Ligands: IOD.24 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.96 Water bridges: A:P.314, A:Q.568 NAG.5: 3 residues within 4Å: Chain A: N.332, S.334, V.335 No protein-ligand interaction detected (PLIP)

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

IOD.6: 6 residues within 4Å: Chain A: A.44, R.45, W.46, N.341, V.342, W.452 Ligand excluded by PLIP IOD.7: 3 residues within 4Å: Chain A: L.199, R.202 Ligands: IOD.41 Ligand excluded by PLIP IOD.8: 2 residues within 4Å: Chain A: D.336, Q.521 Ligand excluded by PLIP IOD.9: 1 residues within 4Å: Chain A: I.387 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain A: N.80, P.145 Ligand excluded by PLIP IOD.11: 1 residues within 4Å: Chain A: S.198 Ligand excluded by PLIP IOD.12: 2 residues within 4Å: Chain A: S.359, A.372 Ligand excluded by PLIP IOD.13: 2 residues within 4Å: Chain A: F.309, W.530 Ligand excluded by PLIP IOD.14: 3 residues within 4Å: Chain A: N.284, H.286, S.592 Ligand excluded by PLIP IOD.15: 2 residues within 4Å: Chain A: L.86, D.87 Ligand excluded by PLIP IOD.16: 4 residues within 4Å: Chain A: K.233, P.234, S.235, E.238 Ligand excluded by PLIP IOD.22: 2 residues within 4Å: Chain A: S.125, F.161 Ligand excluded by PLIP IOD.23: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.24: 4 residues within 4Å: Chain A: N.95, R.96 Ligands: NAG.4, IOD.35 Ligand excluded by PLIP IOD.25: 2 residues within 4Å: Chain A: R.31, Y.331 Ligand excluded by PLIP IOD.26: 2 residues within 4Å: Chain A: Q.217, F.229 Ligand excluded by PLIP IOD.27: 2 residues within 4Å: Chain A: W.220, G.223 Ligand excluded by PLIP IOD.28: 2 residues within 4Å: Chain A: E.373, P.375 Ligand excluded by PLIP IOD.29: 3 residues within 4Å: Chain A: K.462, T.463, G.466 Ligand excluded by PLIP IOD.30: 3 residues within 4Å: Chain A: H.565, A.566, F.567 Ligand excluded by PLIP IOD.31: 2 residues within 4Å: Chain A: P.236, T.425 Ligand excluded by PLIP IOD.32: 1 residues within 4Å: Chain A: P.573 Ligand excluded by PLIP IOD.33: 7 residues within 4Å: Chain A: R.204, N.205, S.208, P.209, L.210, G.211, G.289 Ligand excluded by PLIP IOD.34: 1 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-MAN-MAN.1 Ligand excluded by PLIP IOD.35: 2 residues within 4Å: Chain A: R.506 Ligands: IOD.24 Ligand excluded by PLIP IOD.36: 3 residues within 4Å: Chain A: T.378, N.382, R.385 Ligand excluded by PLIP IOD.37: 4 residues within 4Å: Chain A: R.255, F.381 Ligands: IOD.42, IOD.47 Ligand excluded by PLIP IOD.38: 3 residues within 4Å: Chain A: F.254, S.257, F.381 Ligand excluded by PLIP IOD.39: 2 residues within 4Å: Chain A: E.295, Q.540 Ligand excluded by PLIP IOD.40: 2 residues within 4Å: Chain A: H.377, H.429 Ligand excluded by PLIP IOD.41: 3 residues within 4Å: Chain A: S.198, R.202 Ligands: IOD.7 Ligand excluded by PLIP IOD.42: 3 residues within 4Å: Chain A: F.254, P.424 Ligands: IOD.37 Ligand excluded by PLIP IOD.45: 6 residues within 4Å: Chain A: H.109, R.255, E.258 Ligands: HEM.3, IOD.46, IOD.47 Ligand excluded by PLIP IOD.46: 5 residues within 4Å: Chain A: R.255, E.258 Ligands: HEM.3, IOD.45, IOD.47 Ligand excluded by PLIP IOD.47: 5 residues within 4Å: Chain A: E.258, F.381 Ligands: IOD.37, IOD.45, IOD.46 Ligand excluded by PLIP

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

SCN.17: 2 residues within 4Å: Chain A: D.16, E.17 No protein-ligand interaction detected (PLIP) SCN.18: 6 residues within 4Å: Chain A: E.363, Y.365, R.397, I.559, T.560, K.561 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.561 SCN.19: 5 residues within 4Å: Chain A: S.459, P.461, G.466, T.469, V.470 No protein-ligand interaction detected (PLIP) SCN.20: 3 residues within 4Å: Chain A: N.241, T.242, T.243 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.243 SCN.43: 5 residues within 4Å: Chain A: R.76, N.80, P.149, R.418, N.419 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.76, A:R.418

1 x CA: CALCIUM ION(Non-covalent)

CA.21: 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 EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.44: 4 residues within 4Å: Chain A: Q.468, K.474, I.475, K.478 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.468 Water bridges: A:I.475

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Viswanathan, V. et al., Structure of Yak Lactoperoxidase at 1.55 angstrom Resolution. Protein J. (2021)

Release Date

2020-11-25

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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