SMTL ID : 6lqw.1

Crystal structure of a dimeric yak lactoperoxidase at 2.59 A resolution.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: N.332, V.335 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.332 Water bridges: A:Q.520 NAG.2: 5 residues within 4Å: Chain A: N.95, R.96, I.315, R.504 Ligands: CL.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.95, A:R.96, A:R.96, A:R.504 NAG.7: 4 residues within 4Å: Chain A: N.241, A.244, W.384, K.388 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.241, A:K.388, A:K.388 NAG.8: 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.9: 5 residues within 4Å: Chain B: N.205, S.208, A.214, V.215, Q.217 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:A.214 Hydrogen bonds: B:N.205, B:S.208, B:V.215, B:Q.217 NAG.10: 4 residues within 4Å: Chain B: N.241, A.244, W.384, K.388 No protein-ligand interaction detected (PLIP) NAG.11: 3 residues within 4Å: Chain B: N.332, S.334, V.335 No protein-ligand interaction detected (PLIP) NAG.12: 5 residues within 4Å: Chain B: N.95, R.96, I.315, Q.568 Ligands: CL.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.95, B:R.96

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.3: 20 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, H.351, L.417, Q.423, L.433, I.436, R.440 Ligands: PEO.4 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: 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:L.417, A:L.433, A:L.433, A:I.436 Hydrogen bonds: A:D.112, A:D.112, A:A.114 Salt bridges: A:R.348, A:R.348, A:R.440 Metal complexes: A:H.351 HEM.13: 21 residues within 4Å: Chain B: M.101, G.104, Q.105, D.108, D.112, F.113, A.114, E.258, Q.259, T.344, F.347, R.348, G.350, H.351, V.354, F.380, L.417, L.433, I.436, R.440 Ligands: PEO.14 23 PLIP interactions: 23 interactions with chain B, Hydrophobic interactions: B:Q.105, B:Q.259, B:F.347, B:F.347, B:F.347, B:R.348, B:V.354, B:V.354, B:F.380, B:L.417, B:L.433, B:L.433 Hydrogen bonds: B:D.112, B:D.112, B:A.114 Water bridges: B:T.344, B:R.348, B:R.348, B:R.348 Salt bridges: B:R.348, B:R.348, B:R.440 Metal complexes: B:H.351

2 x PEO: HYDROGEN PEROXIDE(Non-functional Binders)

PEO.4: 3 residues within 4Å: Chain A: Q.105, H.109 Ligands: HEM.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.105, A:H.109 PEO.14: 3 residues within 4Å: Chain B: Q.105, H.109 Ligands: HEM.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.105, B:H.109

2 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:T.184, A:T.184, A:F.186, A:D.188, A:S.190 CA.15: 5 residues within 4Å: Chain B: D.110, T.184, F.186, D.188, S.190 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.110, B:D.110, B:T.184, B:T.184, B:F.186

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

CL.6: 4 residues within 4Å: Chain A: N.95, R.96, R.506 Ligands: NAG.2 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain B: R.506 Ligands: NAG.12 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Viswanathan, V. et al., Crystal structure of a dimeric yak lactoperoxidase at 2.59 A resolution. To Be Published

Release Date

2020-01-29

Peptides

Lactoperoxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lactoperoxidase

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