SMTL ID : 3gck.1

Mode of ligand binding and assignment of subsites in mammalian peroxidases: crystal structure of lactoperoxidase complexes with acetyl salycylic acid, salicylhydroxamic acid and benzylhydroxamic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

monomer

Ligands

2 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(Covalent)

NAG-NAG-MAN.1: 5 residues within 4Å: Chain A: N.95, R.96, I.315, R.504, Q.568 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.3: 4 residues within 4Å: Chain A: N.241, A.244, W.384, K.388 No protein-ligand interaction detected (PLIP)

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: 6 residues within 4Å: Chain A: N.205, S.207, S.208, L.212, V.215, Q.217 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.332, S.334, V.335 No protein-ligand interaction detected (PLIP)

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.5: 24 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: BHO.16 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:Q.105, A:E.258, A:F.347, A:R.348, A:V.354, A:V.354, A:L.376, A:F.380, A:L.417, A:L.433 Hydrogen bonds: A:D.112, A:D.112, A:A.114 Salt bridges: A:R.255, A:R.348, A:R.348, A:R.440 pi-Stacking: A:H.351, A:H.351 pi-Cation interactions: A:H.351 Metal complexes: A:H.351

1 x CA: CALCIUM ION(Non-covalent)

CA.6: 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

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

IOD.7: 5 residues within 4Å: Chain A: R.45, W.46, N.341, V.342, W.452 Ligand excluded by PLIP IOD.8: 3 residues within 4Å: Chain A: N.80, P.145, K.146 Ligand excluded by PLIP IOD.9: 1 residues within 4Å: Chain A: R.504 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain A: Q.217, F.229 Ligand excluded by PLIP IOD.11: 2 residues within 4Å: Chain A: F.309, W.530 Ligand excluded by PLIP IOD.12: 4 residues within 4Å: Chain A: E.363, R.397, I.559, T.560 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.565, F.567 Ligand excluded by PLIP

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

SCN.15: 2 residues within 4Å: Chain A: S.198, L.199 No protein-ligand interaction detected (PLIP)

1 x BHO: BENZHYDROXAMIC ACID(Non-covalent)

BHO.16: 7 residues within 4Å: Chain A: Q.105, H.109, R.255, E.258, F.381, P.424 Ligands: HEM.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.258, A:F.381, A:P.424 Hydrogen bonds: A:Q.105

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, A.K. et al., Mode of ligand binding and assignment of subsites in mammalian peroxidases: crystal structure of lactoperoxidase complexes with acetyl salycylic acid, salicylhydroxamic acid and benzylhydroxamic acid. To be Published

Release Date

2009-03-31

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

Related Entries With Identical Sequence