SMTL ID : 5jqr.1

The Structure of Ascorbate Peroxidase Compound II formed by reaction with m-CPBA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

monomer

Ligands

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

HEM.1: 25 residues within 4Å: Chain A: P.33, L.34, L.36, R.37, W.40, P.131, D.132, A.133, L.140, F.144, L.158, S.159, G.161, H.162, I.164, G.165, A.166, A.167, H.168, R.171, S.172, W.178, L.204, S.206, Y.234 25 PLIP interactions: 24 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:L.36, A:L.36, A:W.40, A:W.40, A:W.40, A:P.131, A:P.131, A:A.133, A:L.140, A:F.144, A:L.158, A:A.167, A:W.178, A:L.204 Hydrogen bonds: A:A.166, A:H.168, A:R.171, A:S.172, A:S.172 Salt bridges: A:R.37, A:H.168, A:H.168 pi-Stacking: A:W.40 Metal complexes: A:H.162, H2O.3

1 x K: POTASSIUM ION(Non-covalent)

K.2: 5 residues within 4Å: Chain A: T.163, T.179, N.181, I.184, D.186 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:T.163, A:T.179, A:N.181, A:I.184

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

SO4.3: 2 residues within 4Å: Chain A: P.126, R.129 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.129 SO4.4: 5 residues within 4Å: Chain A: K.135, G.136, S.137, D.138, H.139 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.136, A:H.139 Water bridges: A:D.138

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kwon, H. et al., Direct visualization of a Fe(IV)-OH intermediate in a heme enzyme. Nat Commun (2016)

Release Date

2016-12-21

Peptides

Ascorbate peroxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ascorbate peroxidase

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