SMTL ID : 3v6q.1

Crystal structure of the complex of bovine lactoperoxidase with Carbon monoxide at 2.0 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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: 4 residues within 4Å: Chain A: N.241, A.244, W.384, K.388 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, F.380, L.417, Q.423, L.433, I.436, R.440 Ligands: BR.15, CMO.20 23 PLIP interactions: 23 interactions with chain A, Hydrophobic interactions: A:Q.105, A:Q.105, A:E.258, A:Q.259, A:F.347, A:F.347, A:F.347, A:R.348, 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.255, A:R.348, A:R.348, A:R.440 Metal complexes: A:H.351

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

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

NAG.4: 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.5: 1 residues within 4Å: Chain A: N.332 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.332

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

IOD.6: 4 residues within 4Å: Chain A: W.46, N.341, V.342, W.452 Ligand excluded by PLIP IOD.7: 2 residues within 4Å: Chain A: N.80, P.145 Ligand excluded by PLIP IOD.8: 2 residues within 4Å: Chain A: P.236, P.424 Ligand excluded by PLIP IOD.9: 2 residues within 4Å: Chain A: F.309, W.530 Ligand excluded by PLIP IOD.10: 5 residues within 4Å: Chain A: E.363, R.397, I.559, T.560, K.561 Ligand excluded by PLIP IOD.11: 2 residues within 4Å: Chain A: Q.217, F.229 Ligand excluded by PLIP IOD.12: 3 residues within 4Å: Chain A: K.462, T.463, G.466 Ligand excluded by PLIP IOD.13: 3 residues within 4Å: Chain A: R.76, P.149, N.419 Ligand excluded by PLIP IOD.14: 1 residues within 4Å: Chain A: S.580 Ligand excluded by PLIP

1 x BR: BROMIDE ION(Non-covalent)

BR.15: 5 residues within 4Å: Chain A: H.109, R.255, E.258 Ligands: HEM.2, CMO.20 Ligand excluded by PLIP

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.16: 3 residues within 4Å: Chain A: S.198, L.199, R.202 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.202

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.17: 3 residues within 4Å: Chain A: H.377, T.378, H.429 3 PLIP interactions: 3 interactions with chain A Water bridges: A:T.378, A:T.378, A:H.429 EDO.18: 5 residues within 4Å: Chain A: E.218, A.219, F.229, V.246, I.387 No protein-ligand interaction detected (PLIP)

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

SCN.19: 3 residues within 4Å: Chain A: N.230, P.236, F.254 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.257

1 x CMO: CARBON MONOXIDE(Non-functional Binders)

CMO.20: 4 residues within 4Å: Chain A: Q.105, H.109 Ligands: HEM.2, BR.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.105 Water bridges: A:R.255

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, A.K. et al., Bovine carbonyl lactoperoxidase structure at 2.0 angstrom resolution and infrared spectra as a function of pH. Protein J. (2012)

Release Date

2012-02-15

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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