SMTL ID : 3ord.1 (1 other biounit)

Structural Evidence for Stabilization of Inhibitor Binding by a Protein Cavity in the Dehaloperoxidase-Hemoglobin from Amphitrite ornata

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.22 Å

Oligo State

monomer

Ligands

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

HEM.1: 19 residues within 4Å: Chain A: F.24, E.31, Y.34, F.35, 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 20 PLIP interactions: 19 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:V.59, A:L.62, A:M.63, A:L.83, A:Q.88, A:L.92, A:N.96, A:F.97, A:F.97, A:L.127 Salt bridges: A:K.58 pi-Cation interactions: A:H.55 Metal complexes: A:H.89, H2O.3

2 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)

2 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, A:D.116 SO4.5: 3 residues within 4Å: Chain A: R.32, V.39, G.40 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.40 Water bridges: A:K.41 Salt bridges: A:R.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de Serrano, V. et al., Structural evidence for stabilization of inhibitor binding by a protein cavity in the dehaloperoxidase-hemoglobin from Amphitrite ornata. Biopolymers (2012)

Release Date

2011-09-07

Peptides

Dehaloperoxidase A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dehaloperoxidase A

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