SMTL ID : 8djt.1

Cytosolic ascorbate peroxidase from Sorghum bicolor - four ascorbates complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.16 Å

Oligo State

monomer

Ligands

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

HEM.1: 31 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: ASC.2, ASC.3, GOL.4 26 PLIP interactions: 25 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:L.37, 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.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, H2O.1

4 x ASC: ASCORBIC ACID(Non-covalent)

ASC.2: 10 residues within 4Å: Chain A: K.30, S.31, C.32, P.34, L.35, I.76, L.80, H.169, R.172 Ligands: HEM.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.35, A:R.172, A:R.172 ASC.3: 11 residues within 4Å: Chain A: W.41, H.42, G.69, A.70, L.131, P.132, D.133, A.134, S.173 Ligands: HEM.1, GOL.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:W.41, A:P.132, A:A.134 Water bridges: A:R.38, A:A.70, A:A.70 ASC.5: 2 residues within 4Å: Chain A: D.75, R.79 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.79, A:R.79 Water bridges: A:D.75, A:D.75 Salt bridges: A:R.79 ASC.6: 8 residues within 4Å: Chain A: T.135, K.136, G.137, P.206, S.207, K.209, A.210, S.213 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.135, A:S.213, A:S.213 Water bridges: A:S.213

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 9 residues within 4Å: Chain A: R.38, W.41, H.42, A.70, L.131, P.132, A.134 Ligands: HEM.1, ASC.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.41 Water bridges: A:H.42

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

NA.7: 5 residues within 4Å: Chain A: T.164, T.180, N.182, P.183, V.185 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.180, A:V.185, A:V.185

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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