SMTL ID : 4nt3.1

Structure of the complex of bovine lactoperoxidase with 3,3'-dipyridyl ketone at 1.99 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 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: ZAW.17 24 PLIP interactions: 23 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:Q.105, A:Q.105, 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 Salt bridges: A:R.348, A:R.348, A:R.440 Metal complexes: A:H.351, H2O.4371 Water bridges: A:F.113, A:A.114, A:R.348, A:R.348

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

1 x NAG- NAG: SUGAR (2-MER)(Post Translational Modification)

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

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

NAG.4: 5 residues within 4Å: Chain A: N.205, S.208, A.214, V.215, Q.217 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.208, A:V.215, A:Q.217, A:Q.217 NAG.5: 2 residues within 4Å: Chain A: N.332, V.335 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.332 NAG.6: 3 residues within 4Å: Chain A: N.95, R.96, Q.568 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.95, A:R.96, A:R.96, A:Q.568 Water bridges: A:N.95

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

IOD.7: 2 residues within 4Å: Chain A: P.236, T.425 Ligand excluded by PLIP IOD.8: 6 residues within 4Å: Chain A: A.44, R.45, W.46, N.341, V.342, W.452 Ligand excluded by PLIP IOD.9: 2 residues within 4Å: Chain A: F.309, W.530 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: R.202 Ligand excluded by PLIP IOD.12: 5 residues within 4Å: Chain A: E.363, R.397, I.559, T.560, K.561 Ligand excluded by PLIP IOD.13: 3 residues within 4Å: Chain A: K.462, T.463, G.466 Ligand excluded by PLIP IOD.14: 2 residues within 4Å: Chain A: H.377, H.429 Ligand excluded by PLIP IOD.15: 3 residues within 4Å: Chain A: N.216, Q.217, F.229 Ligand excluded by PLIP IOD.16: 3 residues within 4Å: Chain A: H.565, A.566, F.567 Ligand excluded by PLIP

1 x ZAW: DI(PYRIDIN-3-YL)METHANONE(Non-covalent)

ZAW.17: 7 residues within 4Å: Chain A: H.109, F.254, R.255, E.258, F.381, Q.423 Ligands: HEM.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.255, A:R.255, A:E.258 Hydrogen bonds: A:Q.423 pi-Stacking: A:F.381

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sirohi, H.V. et al., Structure of the complex of bovine lactoperoxidase with 3,3'-dipyridyl ketone at 1.99 A resolution. To be published

Release Date

2013-12-25

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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