SMTL ID : 4ilz.1 (2 other biounits)

Structural and kinetic study of an internal substrate binding site of dehaloperoxidase-hemoglobin A from Amphitrite ornata

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.91 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, Y.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.100, L.127 Ligands: TBP.11, OXY.12 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:F.24, A:F.35, A:F.35, A:F.35, A:V.59, A:L.62, A:L.83, A:Q.88, A:L.92, A:L.92, A:N.96, A:F.97, A:L.127 Water bridges: A:Q.88 Salt bridges: A:H.55, A:K.58 pi-Stacking: A:H.55 Metal complexes: A:H.89 HEM.13: 19 residues within 4Å: Chain B: F.24, E.31, Y.34, F.35, K.36, 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:K.58, B:V.59, B:L.62, B:L.83, B:Q.88, B:L.92, B:L.92, B:F.97, B:L.100, B:L.127 Hydrogen bonds: B:Q.88 Salt bridges: B:K.36, B:H.55, B:K.58 pi-Cation interactions: B:H.55 Metal complexes: B:H.89, H2O.6

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

SO4.2: 4 residues within 4Å: Chain A: G.1, F.2, K.3, D.116 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.2, A:K.3 Water bridges: A:Q.4, A:S.119 SO4.3: 5 residues within 4Å: Chain A: R.32, V.39, G.40 Ligands: IPA.4, IPA.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.40 Salt bridges: A:R.32 SO4.14: 6 residues within 4Å: Chain B: D.30, E.31, R.33, Y.34, N.96, K.99 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.31, B:N.96 Water bridges: B:Y.34, B:Y.34 Salt bridges: B:R.33, B:K.99 SO4.15: 4 residues within 4Å: Chain B: K.27, Y.28, P.29, D.30 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.27, B:D.30, B:D.30, B:D.30

7 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.4: 4 residues within 4Å: Chain A: L.25, P.29, R.32 Ligands: SO4.3 2 PLIP interactions: 2 interactions with chain A Water bridges: A:P.29, A:R.32 IPA.5: 2 residues within 4Å: Chain A: S.111, G.112 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.112 IPA.6: 7 residues within 4Å: Chain A: M.108, R.109, S.111, Q.113, S.114, F.115 Ligands: IPA.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.113, A:F.115 IPA.7: 2 residues within 4Å: Chain A: L.76, A.77 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.76, A:A.77 Hydrogen bonds: A:A.77, A:S.78 IPA.8: 3 residues within 4Å: Chain A: S.114, F.115 Ligands: IPA.6 No protein-ligand interaction detected (PLIP) IPA.9: 7 residues within 4Å: Chain A: L.22, R.32, K.41, S.42, D.43, L.46 Ligands: SO4.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.22, A:L.46 Hydrogen bonds: A:R.32, A:R.32 Water bridges: A:D.43 IPA.10: 3 residues within 4Å: Chain A: Y.28, P.29, D.30 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.29, A:D.30 Water bridges: A:K.99, A:K.99

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

TBP.11: 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.12 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.21, A:F.24, A:F.60 Halogen bonds: A:I.20, A:V.59

1 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.12: 5 residues within 4Å: Chain A: F.35, H.55, V.59 Ligands: HEM.1, TBP.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.55

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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