SMTL ID : 8dju.1

Cytosolic ascorbate peroxidase from Sorghum bicolor - bicyclic dehydroascorbic acid complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: K.136, G.137, S.138, D.139, H.140 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.137, A:D.139, A:H.140 Water bridges: A:S.138

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

HEM.2: 29 residues within 4Å: Chain A: P.34, L.35, L.37, R.38, W.41, P.132, D.133, A.134, L.141, F.145, I.156, L.159, S.160, G.162, H.163, L.165, G.166, R.167, C.168, H.169, R.172, S.173, F.175, W.179, L.205, S.207, Y.235, L.242 Ligands: SIV.3 25 PLIP interactions: 25 interactions with chain A, Hydrophobic interactions: A:L.37, A:W.41, A:W.41, A:W.41, A:P.132, A:A.134, A:L.141, A:F.145, A:L.159, A:L.159, A:L.165, A:W.179, A:L.205 Hydrogen bonds: A:R.167, A:H.169, A:R.172, A:S.173, A:S.173, A:S.173 Water bridges: A:H.169 Salt bridges: A:R.38, A:H.169, A:H.169 pi-Stacking: A:W.41 Metal complexes: A:H.163

1 x SIV: (3aS,6S,6aR)-3,3,3a,6-tetrahydroxytetrahydrofuro[3,2-b]furan-2(3H)-one (non-preferred name)(Non-covalent)

SIV.3: 9 residues within 4Å: Chain A: S.31, C.32, P.34, L.35, G.166, R.167, H.169, R.172 Ligands: HEM.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:L.35, A:H.169, A:R.172, A:R.172 Water bridges: A:R.167, A:R.167, A:H.169

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 6 residues within 4Å: Chain A: T.164, T.180, N.182, P.183, V.185, D.187 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.180, A:T.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, B. et al., A sorghum ascorbate peroxidase with four binding sites has activity against ascorbate and phenylpropanoids. Plant Physiol. (2023)

Release Date

2023-01-18

Peptides

L-ascorbate peroxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

L-ascorbate peroxidase

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