SMTL ID : 3ixf.2 (1 other biounit)

Crystal Structure of Dehaloperoxidase B at 1.58 and Structural Characterization of the AB Dimer from Amphitrite ornata

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.58 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, N.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: OXY.2 15 PLIP interactions: 14 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:F.24, A:F.35, A:V.59, A:L.62, A:L.83, A:Q.88, A:L.92, A:F.97, A:L.100, A:L.127 Water bridges: A:K.58 Salt bridges: A:H.55, A:K.58 Metal complexes: A:H.89, H2O.5 HEM.7: 19 residues within 4Å: Chain B: F.24, E.31, N.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 20 PLIP interactions: 19 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:F.24, B:F.35, B:F.35, B:V.59, B:V.59, B:L.62, B:M.63, B:L.83, B:Q.88, B:L.92, B:N.96, B:F.97, B:F.97, B:L.127 Hydrogen bonds: B:Q.88 Salt bridges: B:H.55, B:H.55, B:K.58 Metal complexes: B:H.89, H2O.14

1 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.2: 5 residues within 4Å: Chain A: F.21, F.35, H.55, V.59 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.55

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

SO4.3: 4 residues within 4Å: Chain A: G.1, F.2, K.3, D.116 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.1, A:F.2, A:K.3, A:D.116 Water bridges: A:G.1, A:Q.4, A:S.119 SO4.4: 3 residues within 4Å: Chain A: K.32, V.39, G.40 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.40 Water bridges: A:K.32, A:K.41 Salt bridges: A:K.32 SO4.5: 1 residues within 4Å: Chain A: G.95 3 PLIP interactions: 3 interactions with chain A Water bridges: A:T.93, A:T.93 Salt bridges: A:K.99 SO4.6: 1 residues within 4Å: Chain A: K.51 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.51 SO4.8: 2 residues within 4Å: Chain B: K.51, H.55 4 PLIP interactions: 4 interactions with chain B Water bridges: B:K.51, B:K.51 Salt bridges: B:K.51, B:H.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de Serrano, V. et al., Structure of dehaloperoxidase B at 1.58 A resolution and structural characterization of the AB dimer from Amphitrite ornata. Acta Crystallogr.,Sect.D (2010)

Release Date

2010-05-19

Peptides

Dehaloperoxidase B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dehaloperoxidase B

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