SMTL ID : 4ksz.1

Crystal structure of bovine lactoperoxidase complexed with cystiene at 1.98A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

monomer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: N.241, A.244, W.384 No protein-ligand interaction detected (PLIP)

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.2: 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: CYS.19 23 PLIP interactions: 22 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:Q.105, A:Q.105, A:E.258, A:Q.259, A:F.347, A:F.347, A:R.348, A:V.354, A:L.376, A:F.380, A:L.417, A:L.433, A:I.436 Hydrogen bonds: A:D.112, A:A.114 Water bridges: A:R.255, A:R.348, A:R.348 Salt bridges: A:R.348, A:R.348, A:R.440 Metal complexes: A:H.351, H2O.8

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 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 IOD: IODIDE ION(Non-functional Binders)

IOD.4: 2 residues within 4Å: Chain A: N.80, P.145 Ligand excluded by PLIP IOD.5: 3 residues within 4Å: Chain A: P.236, F.239, T.425 Ligand excluded by PLIP IOD.6: 3 residues within 4Å: Chain A: N.216, Q.217, F.229 Ligand excluded by PLIP IOD.7: 6 residues within 4Å: Chain A: A.44, R.45, W.46, N.341, V.342, W.452 Ligand excluded by PLIP IOD.8: 2 residues within 4Å: Chain A: F.309, W.530 Ligand excluded by PLIP IOD.9: 4 residues within 4Å: Chain A: E.363, R.397, I.559, T.560 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain A: H.377, H.429 Ligand excluded by PLIP IOD.11: 2 residues within 4Å: Chain A: R.96 Ligands: NAG.17 Ligand excluded by PLIP IOD.12: 3 residues within 4Å: Chain A: K.462, T.463, G.466 Ligand excluded by PLIP IOD.13: 4 residues within 4Å: Chain A: L.224, A.225, R.271, R.278 Ligand excluded by PLIP IOD.14: 3 residues within 4Å: Chain A: H.565, A.566, F.567 Ligand excluded by PLIP

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.15: 6 residues within 4Å: Chain A: N.205, S.208, L.210, A.214, V.215, Q.217 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.205, A:S.208, A:V.215, A:Q.217, A:Q.217 NAG.16: 3 residues within 4Å: Chain A: N.332, S.334, V.335 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.332 Water bridges: A:S.334 NAG.17: 5 residues within 4Å: Chain A: N.95, R.96, I.315, Q.568 Ligands: IOD.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.96, A:R.96, A:Q.568 Water bridges: A:N.95

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

SCN.18: 2 residues within 4Å: Chain A: S.198, R.202 No protein-ligand interaction detected (PLIP) SCN.20: 3 residues within 4Å: Chain A: P.236, C.248, F.254 No protein-ligand interaction detected (PLIP)

1 x CYS: CYSTEINE(Non-covalent)

CYS.19: 4 residues within 4Å: Chain A: R.255, E.258, F.381 Ligands: HEM.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.423

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, R.P. et al., Crystal structure of bovine lactoperoxidase complexed with cystiene at 1.98A resolution. To be Published

Release Date

2013-07-10

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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