SMTL ID : 2qrb.1

Crystal structure of chloride saturated bovine lactoperoxidase at 2.5 A resolution shows multiple halide binding sites

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 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

NAG-NAG-MAN.1: 4 residues within 4Å: Chain A: N.95, R.96, H.565 Ligands: CL.9 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: 5 residues within 4Å: Chain A: N.205, S.208, A.214, 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 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:D.110, A:T.184, A:F.186, A:S.190

11 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 3 residues within 4Å: Chain A: R.255, E.258 Ligands: HEM.18 Ligand excluded by PLIP CL.7: 6 residues within 4Å: Chain A: A.44, R.45, W.46, N.341, V.342, W.452 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: N.80, P.145 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: R.96 Ligands: NAG-NAG-MAN.1 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: Q.217, P.228, F.229 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: A.225, R.271 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain A: F.309, W.530 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain A: H.377 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain A: E.363, R.397, I.559, T.560 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain A: K.462, T.463 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain A: H.565, F.567 Ligand excluded by PLIP

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

SCN.17: 1 residues within 4Å: Chain A: L.199 No protein-ligand interaction detected (PLIP)

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

HEM.18: 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: CL.6 20 PLIP interactions: 19 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:Q.105, A:Q.105, A:Q.259, 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.348, A:R.440 Metal complexes: A:H.351, H2O.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, A.K. et al., Crystal structure of chloride saturated bovine lactoperoxidase at 2.5 A resolution shows multiple halide binding sites. To be Published

Release Date

2007-08-14

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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