SMTL ID : 4fh7.1

Structure of DHP A in complex with 2,4,6-tribromophenol in 20% methanol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

homo-dimer

Ligands

2 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, Q.88, H.89, L.92, N.96, F.97, L.100, L.127 Ligands: TBP.2, OXY.3 17 PLIP interactions: 17 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:L.92, A:F.97, A:L.127 Hydrogen bonds: A:Q.88 Salt bridges: A:H.55 pi-Stacking: A:H.55 Metal complexes: A:H.89 HEM.12: 20 residues within 4Å: Chain B: F.24, E.31, Y.34, F.35, K.36, 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 21 PLIP interactions: 20 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: B:F.24, B:F.35, B:F.35, B:F.35, B:V.59, B:V.59, B:L.62, B:L.62, B:M.63, B:L.83, B:L.92, B:L.127 Hydrogen bonds: B:Q.88 Water bridges: B:K.58, B:K.58 Salt bridges: B:K.36, B:H.55, B:K.58 pi-Cation interactions: B:H.55 Metal complexes: B:H.89, H2O.8

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

TBP.2: 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.3 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.21, A:F.24, A:F.60 Halogen bonds: A:V.59

1 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.3: 6 residues within 4Å: Chain A: F.21, F.35, H.55, V.59 Ligands: HEM.1, TBP.2 No protein-ligand interaction detected (PLIP)

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

SO4.4: 3 residues within 4Å: Chain A: R.32, V.39, G.40 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.40 Water bridges: A:P.29, A:R.32, A:R.32 Salt bridges: A:R.32 SO4.5: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.116 SO4.6: 1 residues within 4Å: Chain A: K.99 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.95, A:K.99 Salt bridges: A:K.99 SO4.7: 2 residues within 4Å: Chain A: T.15, K.47 4 PLIP interactions: 4 interactions with chain A Water bridges: A:Q.18, A:Q.18, A:K.47 Salt bridges: A:K.47 SO4.8: 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:Q.4, A:D.72, A:S.119 SO4.10: 3 residues within 4Å: Chain A: R.109, S.117, Q.118 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.117, A:S.117, A:Q.118 Water bridges: A:D.116 Salt bridges: A:R.109 SO4.13: 2 residues within 4Å: Chain B: M.86, K.87 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.87 Water bridges: B:Q.88, B:Q.88 SO4.14: 2 residues within 4Å: Chain B: N.81, T.82 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.81 Water bridges: B:T.82, B:T.82

4 x MOH: METHANOL(Non-functional Binders)

MOH.9: 2 residues within 4Å: Chain A: S.132, S.133 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.133 Water bridges: A:S.133, A:S.133 MOH.11: 1 residues within 4Å: Chain A: S.114 1 PLIP interactions: 1 interactions with chain A Water bridges: A:F.115 MOH.15: 1 residues within 4Å: Chain B: K.51 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.51 MOH.16: 3 residues within 4Å: Chain B: D.12, T.15, Y.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.12, B:D.12

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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