SMTL ID : 5lk9.1

Dehaloperoxidase B from Amphitrite ornata: indazole complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.12 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, 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: LZ1.5 18 PLIP interactions: 17 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:F.24, A:F.35, A:V.59, A:V.59, A:L.62, A:L.83, A:Q.88, A:L.92, A:N.96, A:F.97, A:L.127 Hydrogen bonds: A:Y.38 Water bridges: A:N.37 Salt bridges: A:H.55, A:H.55, A:K.58 Metal complexes: A:H.89, H2O.1 HEM.7: 18 residues within 4Å: Chain B: F.24, E.31, N.34, F.35, H.55, K.58, V.59, M.63, L.83, M.86, Q.88, H.89, L.92, N.96, F.97, L.100, L.127 Ligands: LZ1.10 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:F.24, B:F.35, B:V.59, B:V.59, B:M.63, B:L.83, B:Q.88, B:L.92, B:N.96, B:F.97, B:L.100, B:L.127 Hydrogen bonds: B:Q.88 Water bridges: B:Q.88 Salt bridges: B:H.55, B:H.55, B:K.58 Metal complexes: B:H.89

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

SO4.2: 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.41, A:K.41 Salt bridges: A:K.32 SO4.3: 3 residues within 4Å: Chain A: G.1, F.2, K.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:F.2, A:K.3 Water bridges: A:Q.4, A:S.119, A:S.119, A:S.119 SO4.6: 2 residues within 4Å: Chain B: G.95, K.99 6 PLIP interactions: 6 interactions with chain B Water bridges: B:T.93, B:G.95, B:G.95, B:E.98, B:K.99 Salt bridges: B:K.99 SO4.8: 3 residues within 4Å: Chain B: K.32, V.39, G.40 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.40 Water bridges: B:K.41, B:K.41 Salt bridges: B:K.32

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: Q.4, D.5, T.8, Q.113, S.114, F.115 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.4, A:Q.4, A:D.5 Water bridges: A:D.116 GOL.9: 6 residues within 4Å: Chain B: Q.4, D.5, T.8, Q.113, S.114, F.115 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.4, B:T.8, B:S.114 Water bridges: B:D.116

2 x LZ1: 1H-indazole

LZ1.5: 7 residues within 4Å: Chain A: F.21, F.35, Y.38, H.55, T.56, V.59 Ligands: HEM.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.35, A:V.59, A:V.59 Hydrogen bonds: A:Y.38 pi-Stacking: A:F.21 LZ1.10: 6 residues within 4Å: Chain B: F.21, F.35, H.55, T.56, V.59 Ligands: HEM.7 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.21, B:F.35, B:F.35, B:V.59, B:V.59 pi-Stacking: B:F.21

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2017-08-02

Peptides

Dehaloperoxidase B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dehaloperoxidase B

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