SMTL ID : 7y3u.1

Crystal structure of the complex of Lactoperoxidase with Nitric oxide at 2.50A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 3 residues within 4Å: Chain A: N.95, R.96, R.504 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.504 NAG-NAG-BMA.2: 8 residues within 4Å: Chain B: N.205, S.208, L.210, L.212, A.214, V.215, Q.217, W.220 No protein-ligand interaction detected (PLIP)

2 x MH0: Mesoheme(Covalent)

MH0.3: 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: NO.9 24 PLIP interactions: 23 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Q.105, A:D.108, A:Q.259, A:F.347, A:F.347, 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.255, A:T.344, A:R.348 Salt bridges: A:R.255, A:R.348, A:R.440 Metal complexes: A:H.351, NO.9 MH0.11: 23 residues within 4Å: Chain B: 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: NO.16 23 PLIP interactions: 23 interactions with chain B, Hydrophobic interactions: B:Q.105, B:D.108, 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, B:I.436 Hydrogen bonds: B:D.112, B:A.114 Water bridges: B:R.255, B:T.344, B:R.348 Salt bridges: B:R.348, B:R.348, B:R.440 Metal complexes: B:H.351

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 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:T.184, A:F.186 CA.12: 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:S.190

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

CL.5: 6 residues within 4Å: Chain A: R.45, W.46, N.341, V.342, M.446, W.452 Ligand excluded by PLIP

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

NAG.6: 3 residues within 4Å: Chain A: N.332, S.334, V.335 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.332 NAG.7: 5 residues within 4Å: Chain A: N.241, T.243, A.244, W.384, K.388 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.241, A:A.244 NAG.8: 7 residues within 4Å: Chain A: N.205, S.208, L.210, L.212, A.214, V.215, Q.217 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.208, A:V.215, A:Q.217 NAG.13: 3 residues within 4Å: Chain B: N.95, I.315, Q.568 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.96 NAG.14: 4 residues within 4Å: Chain B: N.241, T.243, A.244, W.384 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.241, B:T.243 NAG.15: 3 residues within 4Å: Chain B: N.332, S.334, V.335 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.332, B:N.332

2 x NO: NITRIC OXIDE(Non-covalent)

NO.9: 4 residues within 4Å: Chain A: Q.105, H.109, H.351 Ligands: MH0.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.105 Water bridges: A:H.109 NO.16: 4 residues within 4Å: Chain B: Q.105, H.109, H.351 Ligands: MH0.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.105 Water bridges: B:H.109

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.10: 5 residues within 4Å: Chain B: L.199, A.251, G.252, D.253, F.254 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.199, B:F.254 Hydrogen bonds: B:F.254

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, P.K. et al., Crystal structure of the complex of Lactoperoxidase with Nitric oxide at 2.50A resolution. To Be Published

Release Date

2022-06-29

Peptides

Lactoperoxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lactoperoxidase

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