SMTL ID : 5k1l.1

Dehaloperoxidase B from Amphitrite ornata: benzimidazole complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.08 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 18 residues within 4Å: Chain A: F.24, E.31, N.34, F.35, Y.38, H.55, K.58, V.59, M.63, L.83, M.86, Q.88, H.89, L.92, N.96, F.97, L.127 Ligands: BZI.2 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:F.24, A:F.35, A:F.35, A:V.59, A:M.63, A:L.83, A:Q.88, A:L.92, A:L.92, A:N.96, A:F.97, A:L.127 Salt bridges: A:H.55, A:H.55, A:K.58 Metal complexes: A:H.89 HEM.4: 18 residues within 4Å: Chain B: F.24, E.31, N.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.127 Ligands: BZI.5 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:F.24, 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:L.92, B:N.96, B:L.127 Hydrogen bonds: B:Q.88 Water bridges: B:N.37 Salt bridges: B:H.55, B:H.55 pi-Cation interactions: B:H.89 Metal complexes: B:H.89

2 x BZI: BENZIMIDAZOLE(Non-covalent)

BZI.2: 5 residues within 4Å: Chain A: F.21, F.35, V.59, L.100 Ligands: HEM.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.21, A:V.59, A:L.100 BZI.5: 5 residues within 4Å: Chain B: F.21, F.35, V.59, L.100 Ligands: HEM.4 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.21, B:V.59, B:L.100 Water bridges: B:H.55

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

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moreno Chicano, T. et al., Dehaloperoxidase B from Amphitrite ornata: benzimidazole complex. to be published

Release Date

2017-06-07

Peptides

Dehaloperoxidase B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dehaloperoxidase B

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