SMTL ID : 3r55.1

Crystal structure of the complex of goat lactoperoxidase with Pyrazinamide at 2.1 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

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.1: 6 residues within 4Å: Chain A: N.205, S.208, L.210, A.214, V.215, Q.217 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.241, A.244, W.384, K.388 No protein-ligand interaction detected (PLIP)

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

NAG.3: 4 residues within 4Å: Chain A: N.95, R.96, I.315 Ligands: IOD.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.95, A:R.96 NAG.4: 3 residues within 4Å: Chain A: N.332, S.334, V.335 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.332 Water bridges: A:N.332, A:D.336, A:D.524

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.5: 26 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, Y.312, 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: PZA.21, PZA.22 27 PLIP interactions: 27 interactions with chain A, Hydrophobic interactions: A:Q.105, A:Q.105, A:D.108, A:E.258, A:Q.259, A:F.347, A:F.347, A:F.347, A:R.348, A:V.354, A:V.354, A:L.376, 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.255, A:R.348, A:R.348, A:R.348 Salt bridges: A:R.255, A:R.348, A:R.440 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:D.110, A:T.184, A:F.186, A:S.190

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 2 residues within 4Å: Chain A: H.222, H.558 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.222, A:H.558

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

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: 3 residues within 4Å: Chain A: N.216, Q.217, F.229 Ligand excluded by PLIP IOD.10: 4 residues within 4Å: Chain A: E.363, R.397, I.559, T.560 Ligand excluded by PLIP IOD.11: 2 residues within 4Å: Chain A: N.80, P.145 Ligand excluded by PLIP IOD.12: 3 residues within 4Å: Chain A: R.96, R.506 Ligands: NAG.3 Ligand excluded by PLIP IOD.13: 2 residues within 4Å: Chain A: F.309, W.530 Ligand excluded by PLIP IOD.14: 3 residues within 4Å: Chain A: K.462, T.463, G.466 Ligand excluded by PLIP IOD.15: 4 residues within 4Å: Chain A: D.311, H.565, A.566, F.567 Ligand excluded by PLIP IOD.16: 2 residues within 4Å: Chain A: L.224, A.225 Ligand excluded by PLIP IOD.17: 3 residues within 4Å: Chain A: E.373, L.374, P.375 Ligand excluded by PLIP IOD.18: 2 residues within 4Å: Chain A: P.236, T.425 Ligand excluded by PLIP IOD.19: 2 residues within 4Å: Chain A: R.31, Y.331 Ligand excluded by PLIP

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

SCN.20: 3 residues within 4Å: Chain A: N.230, P.236, C.248 No protein-ligand interaction detected (PLIP)

2 x PZA: PYRAZINE-2-CARBOXAMIDE(Non-covalent)

PZA.21: 7 residues within 4Å: Chain A: Q.105, D.108, H.109, R.255, E.258 Ligands: HEM.5, PZA.22 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.105 Water bridges: A:R.255, A:R.255 PZA.22: 7 residues within 4Å: Chain A: S.254, R.255, E.258, F.381, Q.423 Ligands: HEM.5, PZA.21 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.423

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

EDO.23: 2 residues within 4Å: Chain A: H.377, H.429 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.377 EDO.24: 5 residues within 4Å: Chain A: S.33, A.35, L.36, R.41, R.338 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.33, A:S.33 Water bridges: A:A.35, A:A.35, A:G.37, A:A.42, A:R.338 EDO.25: 4 residues within 4Å: Chain A: I.24, P.197, A.200, S.201 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.197 EDO.26: 4 residues within 4Å: Chain A: A.219, F.229, V.246, I.387 No protein-ligand interaction detected (PLIP) EDO.27: 5 residues within 4Å: Chain A: S.359, L.361, P.367, E.373, K.402 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.359, A:K.402

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.28: 6 residues within 4Å: Chain A: R.76, N.80, P.149, K.150, R.418, N.419 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.80, A:R.418, A:N.419 GOL.29: 8 residues within 4Å: Chain A: E.123, S.125, C.129, G.136, D.137, E.138, C.139, F.161 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.125, A:E.138, A:C.139

1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.30: 3 residues within 4Å: Chain A: S.198, L.199, R.202 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:R.202

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.31: 4 residues within 4Å: Chain A: K.81, K.479, D.482, L.483 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.479 Water bridges: A:K.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, R.P. et al., Crystal structure of the complex of goat lactoperoxidase with Pyrazinamide at 2.1 A resolution. To be Published

Release Date

2011-08-03

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

Related Entries With Identical Sequence