SMTL ID : 6l3z.1

Crystal structure of yak lactoperoxidase with partially coordinated Na ion in the distal heme cavity.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

4 x NAG: N-ACETYL-D-GLUCOSAMINE(Post Translational Modification)

NAG.1: 3 residues within 4Å: Chain A: N.95, I.315 Ligands: PO4.7 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.96 NAG.2: 5 residues within 4Å: Chain A: N.205, S.208, A.214, V.215, Q.217 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.208, A:V.215, A:Q.217, A:Q.217 Water bridges: A:N.205 NAG.3: 3 residues within 4Å: Chain A: N.241, A.244, W.384 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.244 Water bridges: A:W.384 NAG.11: 3 residues within 4Å: Chain A: N.332, S.334, V.335 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.332

3 x CA: CALCIUM ION(Non-covalent)

CA.4: 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:F.186, A:D.188, A:S.190 CA.8: 2 residues within 4Å: Chain A: H.222, H.558 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.222, A:H.558 CA.9: 6 residues within 4Å: Chain A: A.44, R.45, W.46, N.341, V.342, W.452 No protein-ligand interaction detected (PLIP)

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.5: 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: NA.6 24 PLIP interactions: 23 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:Q.105, A:Q.105, A:D.108, 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 Salt bridges: A:R.348, A:R.348, A:R.440 Water bridges: A:A.114, A:H.444 Metal complexes: A:H.351, H2O.2

1 x NA: SODIUM ION(Non-functional Binders)

NA.6: 3 residues within 4Å: Chain A: H.109, R.255 Ligands: HEM.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.255 Water bridges: A:R.255

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.7: 5 residues within 4Å: Chain A: N.95, R.96, R.504, R.506 Ligands: NAG.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.95, A:R.504 Salt bridges: A:R.96, A:R.506 Water bridges: A:R.96

1 x F: FLUORIDE ION(Non-covalent)

F.10: 3 residues within 4Å: Chain A: A.35, R.41, R.338 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 with partially coordinated Na ion in the distal heme cavity. To Be Published

Release Date

2019-10-30

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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