SMTL ID : 4fh6.1

Structure of DHP A in complex with 2,4,6-tribromophenol in 10% DMSO

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.44 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 21 residues within 4Å: Chain A: F.24, E.31, Y.34, F.35, D.54, 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: TBP.3, OXY.4 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:F.24, A:F.35, A:F.35, A:V.59, A:L.62, A:L.62, A:M.63, A:L.83, A:Q.88, A:L.92, A:N.96, A:F.97, A:L.127 Hydrogen bonds: A:Q.88 Salt bridges: A:H.55, A:K.58 pi-Stacking: A:H.55 Metal complexes: A:H.89 HEM.5: 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.127 Ligands: TBP.7, OXY.9 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:F.24, B:F.35, B:V.59, B:L.62, B:L.62, B:M.63, B:L.83, B:Q.88, B:L.92, B:L.92, B:F.97, B:F.97, B:L.127 Hydrogen bonds: B:Q.88 Salt bridges: B:K.51, B:H.55, B:K.58 pi-Stacking: B:H.55 Metal complexes: B:H.89

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

SO4.2: 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 SO4.6: 4 residues within 4Å: Chain B: G.1, F.2, K.3, D.116 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:F.2, B:K.3, B:D.116 Water bridges: B:G.1, B:Q.4, B:S.119 SO4.10: 5 residues within 4Å: Chain B: E.31, R.33, Y.34, N.96, K.99 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.31, B:R.33, B:Y.34, B:N.96 Water bridges: B:T.93, B:T.93 Salt bridges: B:K.99

2 x TBP: 2,4,6-TRIBROMOPHENOL(Covalent)

TBP.3: 10 residues within 4Å: Chain A: I.20, F.21, F.24, F.35, V.59, F.60, M.63, L.100 Ligands: HEM.1, OXY.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.21, A:F.24, A:F.60 TBP.7: 11 residues within 4Å: Chain B: F.21, F.24, F.35, V.59, M.63, N.96, F.97, K.99, L.100 Ligands: HEM.5, OXY.9 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.24

2 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.4: 6 residues within 4Å: Chain A: F.21, F.35, H.55, V.59 Ligands: HEM.1, TBP.3 No protein-ligand interaction detected (PLIP) OXY.9: 6 residues within 4Å: Chain B: F.21, F.35, H.55, V.59 Ligands: HEM.5, TBP.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.55

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.8: 5 residues within 4Å: Chain B: F.35, K.36, N.37, Y.38, V.39 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.37 Water bridges: B:Y.38

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, J. et al., Structural and Kinetic Study of an Internal Substrate Binding Site in Dehaloperoxidase-Hemoglobin A from Amphitrite ornata. Biochemistry (2013)

Release Date

2013-03-27

Peptides

Dehaloperoxidase A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dehaloperoxidase A

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