SMTL ID : 4y55.1

Crystal structure of Buffalo lactoperoxidase with Rhodanide at 2.09 Angstrom resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 6 residues within 4Å: Chain A: N.95, R.96, I.315, R.504, H.565, Q.568 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.504

2 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: 7 residues within 4Å: Chain A: N.205, S.208, L.210, A.214, V.215, Q.217, W.220 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.217, A:Q.217 NAG-NAG.4: 1 residues within 4Å: Chain A: N.332 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN.3: 4 residues within 4Å: Chain A: N.241, A.244, W.384, K.388 No protein-ligand interaction detected (PLIP)

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:T.184, A:T.184, A:F.186, A:S.190

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

IOD.6: 2 residues within 4Å: Chain A: N.216, F.229 Ligand excluded by PLIP IOD.7: 2 residues within 4Å: Chain A: P.236, P.424 Ligand excluded by PLIP IOD.8: 5 residues within 4Å: Chain A: E.363, R.397, I.559, T.560, K.561 Ligand excluded by PLIP IOD.9: 6 residues within 4Å: Chain A: A.44, R.45, W.46, N.341, V.342, W.452 Ligand excluded by PLIP IOD.10: 3 residues within 4Å: Chain A: K.462, T.463, G.466 Ligand excluded by PLIP IOD.20: 2 residues within 4Å: Chain A: F.309, W.530 Ligand excluded by PLIP

4 x NO3: NITRATE ION(Non-functional Binders)

NO3.11: 4 residues within 4Å: Chain A: Y.85, L.86, D.87, K.411 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.86, A:D.87, A:D.87 NO3.12: 4 residues within 4Å: Chain A: R.31, Y.331, N.333, R.527 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.31, A:N.333 NO3.13: 4 residues within 4Å: Chain A: E.77, N.80, K.81, P.145 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.77, A:N.80 NO3.14: 3 residues within 4Å: Chain A: H.377, T.378, H.429 No protein-ligand interaction detected (PLIP)

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.15: 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: SCN.18 22 PLIP interactions: 21 interactions with chain A, 1 Ligand-Water interactions, 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 Hydrogen bonds: A:D.112, A:A.114 Water bridges: A:R.348, A:R.348 Salt bridges: A:R.255, A:R.348, A:R.440 Metal complexes: A:H.351, H2O.7

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

SCN.16: 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.17: 4 residues within 4Å: Chain A: R.76, P.149, K.150, N.419 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.76, A:N.419 SCN.18: 4 residues within 4Å: Chain A: H.109, R.255, E.258 Ligands: HEM.15 No protein-ligand interaction detected (PLIP) SCN.19: 3 residues within 4Å: Chain A: S.198, L.199, R.202 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gupta, A. et al., Crystal structure of Buffalo lactoperoxidase with Rhodanide at 2.09 Angstrom resolution. To Be Published

Release Date

2015-03-25

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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