SMTL ID : 3mou.1

Characterization of the Inhibitor Binding Site of the Dehaloperoxidase-Hemoglobin from Amphitrite ornata using High-Pressure Xenon Derivatization

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

homo-dimer

Ligands

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 20 residues within 4Å: Chain A: F.24, E.31, Y.34, F.35, Y.38, H.55, K.58, V.59, L.62, M.63, L.83, M.86, Q.88, H.89, L.92, N.96, F.97, L.100, L.127 Ligands: XE.2 22 PLIP interactions: 21 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:F.24, A:Y.34, A:F.35, A:F.35, A:K.58, A:V.59, A:L.62, A:L.62, A:M.63, A:L.83, A:Q.88, A:L.92, A:L.92, A:F.97, A:L.100, A:L.127 Hydrogen bonds: A:Y.38 Salt bridges: A:H.55, A:K.58 pi-Cation interactions: A:H.55 Metal complexes: A:H.89, H2O.6 HEM.8: 20 residues within 4Å: Chain B: F.24, E.31, Y.34, F.35, Y.38, H.55, K.58, V.59, L.62, M.63, L.83, M.86, Q.88, H.89, L.92, N.96, F.97, L.100, L.127 Ligands: XE.9 21 PLIP interactions: 20 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:F.24, B:F.35, B:F.35, B:K.58, B:V.59, B:L.62, B:L.62, B:L.83, B:Q.88, B:L.92, B:L.92, B:F.97, B:L.100, B:L.127 Hydrogen bonds: B:Y.38, B:Q.88 Salt bridges: B:H.55, B:K.58 pi-Stacking: B:H.55 Metal complexes: B:H.89, H2O.11

4 x XE: XENON(Non-covalent)

XE.2: 2 residues within 4Å: Chain A: F.21 Ligands: HEM.1 No protein-ligand interaction detected (PLIP) XE.3: 4 residues within 4Å: Chain A: L.62, V.66, D.79, T.82 No protein-ligand interaction detected (PLIP) XE.9: 3 residues within 4Å: Chain B: F.21, L.100 Ligands: HEM.8 No protein-ligand interaction detected (PLIP) XE.10: 4 residues within 4Å: Chain B: L.62, V.66, D.79, T.82 No protein-ligand interaction detected (PLIP)

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 4 residues within 4Å: Chain A: G.1, F.2, K.3, D.116 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.2, A:K.3 Water bridges: A:S.119 SO4.5: 3 residues within 4Å: Chain A: Y.28, P.29, D.30 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.27, A:D.30 SO4.6: 7 residues within 4Å: Chain A: R.32, V.39, G.40 Chain B: G.1, F.2, K.3, D.116 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:G.40, B:F.2, B:K.3, B:D.116 Salt bridges: A:R.32 Water bridges: B:G.1, B:Q.4, B:S.119 SO4.7: 5 residues within 4Å: Chain B: E.31, R.33, Y.34, N.96, K.99 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.31, B:R.33, B:Y.34, B:N.96 Water bridges: B:T.93 Salt bridges: B:K.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de Serrano, V.S. et al., Characterization of the Inhibitor Binding Site of the Dehaloperoxidase-Hemoglobin from Amphitrite ornata using High-Pressure Xenon Derivatization. To be Published

Release Date

2011-04-20

Peptides

Dehaloperoxidase A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dehaloperoxidase A

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