SMTL ID : 6l2j.1

Crystal structure of yak lactoperoxidase at 1.93 A resolution.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.93 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: 9 residues within 4Å: Chain A: N.205, S.208, L.210, A.214, V.215, Q.217, W.220 Ligands: PEO.45, PEO.46 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.217, A:W.220, A:W.220 Hydrogen bonds: A:Q.217

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, F.380, L.417, Q.423, L.433, I.436, R.440 Ligands: IOD.14, OSM.38, PEO.42 26 PLIP interactions: 26 interactions with chain A, Hydrophobic interactions: A:Q.105, A:Q.105, 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:E.116, 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

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.47 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.96 Water bridges: A:R.96, A:P.314 NAG.5: 4 residues within 4Å: Chain A: N.332, S.334, V.335 Ligands: IOD.9 No protein-ligand interaction detected (PLIP)

26 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: R.255, F.381 Ligands: OSM.38 Ligand excluded by PLIP IOD.8: 2 residues within 4Å: Chain A: R.202 Ligands: OSM.39 Ligand excluded by PLIP IOD.9: 4 residues within 4Å: Chain A: V.335, D.336, Q.521 Ligands: NAG.5 Ligand excluded by PLIP IOD.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.11: 3 residues within 4Å: Chain A: W.220, G.223 Ligands: SCN.28 Ligand excluded by PLIP IOD.12: 3 residues within 4Å: Chain A: N.80, P.145 Ligands: SCN.29 Ligand excluded by PLIP IOD.13: 2 residues within 4Å: Chain A: E.196, S.198 Ligand excluded by PLIP IOD.14: 6 residues within 4Å: Chain A: H.109, R.255, E.258 Ligands: HEM.3, OSM.38, PEO.42 Ligand excluded by PLIP IOD.15: 1 residues within 4Å: Chain A: S.359 Ligand excluded by PLIP IOD.16: 5 residues within 4Å: Chain A: K.462, T.463, G.466 Ligands: SCN.26, SCN.30 Ligand excluded by PLIP IOD.17: 3 residues within 4Å: Chain A: F.309, W.530 Ligands: SCN.31 Ligand excluded by PLIP IOD.18: 3 residues within 4Å: Chain A: N.284, H.286, S.592 Ligand excluded by PLIP IOD.19: 3 residues within 4Å: Chain A: P.236, T.425 Ligands: SCN.27 Ligand excluded by PLIP IOD.20: 2 residues within 4Å: Chain A: L.86, D.87 Ligand excluded by PLIP IOD.21: 4 residues within 4Å: Chain A: K.233, P.234, S.235, E.238 Ligand excluded by PLIP IOD.22: 3 residues within 4Å: Chain A: Q.217, F.229 Ligands: SCN.34 Ligand excluded by PLIP IOD.47: 4 residues within 4Å: Chain A: N.95, R.96 Ligands: NAG.4, IOD.59 Ligand excluded by PLIP IOD.53: 3 residues within 4Å: Chain A: H.565, A.566, F.567 Ligand excluded by PLIP IOD.54: 4 residues within 4Å: Chain A: K.126, P.159, S.161, H.426 Ligand excluded by PLIP IOD.55: 3 residues within 4Å: Chain A: L.119, S.125, K.126 Ligand excluded by PLIP IOD.56: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.57: 3 residues within 4Å: Chain A: E.373, P.375 Ligands: SCN.32 Ligand excluded by PLIP IOD.58: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.59: 2 residues within 4Å: Chain A: R.506 Ligands: IOD.47 Ligand excluded by PLIP IOD.60: 3 residues within 4Å: Chain A: R.31, Y.331, N.333 Ligand excluded by PLIP

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

SCN.23: 5 residues within 4Å: Chain A: N.230, P.236, C.248, S.254 Ligands: PEO.43 No protein-ligand interaction detected (PLIP) SCN.24: 2 residues within 4Å: Chain A: D.16, E.17 No protein-ligand interaction detected (PLIP) SCN.25: 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.26: 7 residues within 4Å: Chain A: S.459, P.461, G.466, T.469, V.470 Ligands: IOD.16, SCN.30 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.470 SCN.27: 6 residues within 4Å: Chain A: P.234, S.235, P.236, F.239, T.425 Ligands: IOD.19 No protein-ligand interaction detected (PLIP) SCN.28: 4 residues within 4Å: Chain A: W.220, H.222, G.223 Ligands: IOD.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.223 SCN.29: 6 residues within 4Å: Chain A: N.80, K.81, P.145, N.147, D.148 Ligands: IOD.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.80 Water bridges: A:N.147 SCN.30: 5 residues within 4Å: Chain A: K.462, T.463, G.466 Ligands: IOD.16, SCN.26 No protein-ligand interaction detected (PLIP) SCN.31: 5 residues within 4Å: Chain A: I.306, F.309, R.310, W.530 Ligands: IOD.17 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.523 SCN.32: 5 residues within 4Å: Chain A: T.357, E.373, L.374, P.375 Ligands: IOD.57 No protein-ligand interaction detected (PLIP) SCN.33: 3 residues within 4Å: Chain A: N.241, T.242, T.243 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.242, A:T.242, A:T.243 Water bridges: A:T.243 SCN.34: 5 residues within 4Å: Chain A: N.216, Q.217, E.218, F.229 Ligands: IOD.22 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.216

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

OSM.35: 5 residues within 4Å: Chain A: R.76, N.80, P.149, R.418, N.419 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.76, A:R.418, A:N.419, A:N.419 OSM.36: 1 residues within 4Å: Chain A: D.488 No protein-ligand interaction detected (PLIP) OSM.37: 9 residues within 4Å: Chain A: R.204, N.205, L.206, S.208, P.209, L.210, G.211, G.289, E.290 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.210, A:G.211 Water bridges: A:N.205, A:L.212 OSM.38: 7 residues within 4Å: Chain A: R.255, E.258, F.381 Ligands: HEM.3, IOD.7, IOD.14, PEO.42 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.423 OSM.39: 4 residues within 4Å: Chain A: S.198, L.199, R.202 Ligands: IOD.8 No protein-ligand interaction detected (PLIP) OSM.40: 5 residues within 4Å: Chain A: V.13, T.23, I.24, T.25 Ligands: OSM.61 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.24, A:T.25 OSM.41: 4 residues within 4Å: Chain A: Q.468, K.474, I.475, K.478 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.468 OSM.61: 5 residues within 4Å: Chain A: I.24, P.197, A.200, S.201 Ligands: OSM.40 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.197, A:S.201 Water bridges: A:R.204, A:R.204

5 x PEO: HYDROGEN PEROXIDE(Non-functional Binders)

PEO.42: 6 residues within 4Å: Chain A: Q.105, H.109, H.351 Ligands: HEM.3, IOD.14, OSM.38 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.105, A:H.109, A:H.351 Water bridges: A:R.255 PEO.43: 7 residues within 4Å: Chain A: C.248, S.254, R.255, A.256, S.257, F.381 Ligands: SCN.23 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.257, A:S.257 Water bridges: A:A.256, A:A.256 PEO.44: 3 residues within 4Å: Chain A: W.287, E.295, Q.540 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.295, A:Q.540 Water bridges: A:K.291, A:R.593, A:R.593 PEO.45: 3 residues within 4Å: Chain A: S.208 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.1, PEO.46 No protein-ligand interaction detected (PLIP) PEO.46: 4 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN.1, PEO.45 No protein-ligand interaction detected (PLIP)

5 x CA: CALCIUM ION(Non-covalent)

CA.48: 2 residues within 4Å: Chain A: L.224, A.225 No protein-ligand interaction detected (PLIP) CA.49: 2 residues within 4Å: Chain A: D.410, N.473 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.410, H2O.16 CA.50: 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 CA.51: 3 residues within 4Å: Chain A: A.35, R.41, R.338 No protein-ligand interaction detected (PLIP) CA.52: 3 residues within 4Å: Chain A: T.378, N.382, R.385 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Viswanathan, V. et al., Crystal structure of yak lactoperoxidase at 1.93 A resolution. To Be Published

Release Date

2019-10-30

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase