SMTL ID : 6xv4.1

Neutron structure of ferric ascorbate peroxidase-ascorbate complex

Coordinates

PDB Format

Method

NEUTRON DIFFRACTION 2.09 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 30 residues within 4Å: Chain A: P.45, L.46, L.48, R.49, W.52, P.143, D.144, A.145, L.152, F.156, I.167, L.170, S.171, G.173, H.174, I.176, G.177, A.178, A.179, H.180, R.183, S.184, G.185, F.186, W.190, L.216, S.218, Y.246, L.253 Ligands: ASC.5 29 PLIP interactions: 27 interactions with chain A, 2 Ligand-Water interactions Hydrophobic interactions: A:L.48, A:W.52, A:W.52, A:P.143, A:P.143, A:A.145, A:L.152, A:F.156, A:F.156, A:L.170, A:L.170, A:A.179, A:W.190, A:L.216 Hydrogen bonds: A:A.178, A:H.180, A:R.183, A:S.184, A:S.184, A:S.184 Water bridges: A:R.49, A:H.180 Salt bridges: A:R.49, A:H.180, A:H.180 pi-Stacking: A:W.52 Metal complexes: A:H.174, H2O.3, H2O.3 HEM.6: 30 residues within 4Å: Chain B: P.45, L.46, L.48, R.49, W.52, P.143, D.144, A.145, L.152, F.156, I.167, L.170, S.171, G.173, H.174, I.176, G.177, A.178, A.179, H.180, R.183, S.184, G.185, F.186, W.190, L.216, S.218, Y.246, L.253 Ligands: ASC.10 29 PLIP interactions: 27 interactions with chain B, 2 Ligand-Water interactions Hydrophobic interactions: B:L.48, B:W.52, B:W.52, B:P.143, B:P.143, B:A.145, B:L.152, B:F.156, B:F.156, B:L.170, B:L.170, B:A.179, B:W.190, B:L.216 Hydrogen bonds: B:A.178, B:H.180, B:R.183, B:S.184, B:S.184, B:S.184 Water bridges: B:R.49, B:H.180 Salt bridges: B:R.49, B:H.180, B:H.180 pi-Stacking: B:W.52 Metal complexes: B:H.174, H2O.17, H2O.17

2 x K: POTASSIUM ION(Non-covalent)

K.2: 6 residues within 4Å: Chain A: T.175, T.191, N.193, I.196, D.198, S.200 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.175, A:T.191, A:N.193, A:I.196, A:D.198 K.7: 6 residues within 4Å: Chain B: T.175, T.191, N.193, I.196, D.198, S.200 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:T.175, B:T.191, B:N.193, B:I.196, B:D.198

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

SO4.3: 3 residues within 4Å: Chain A: P.138, R.141 Chain B: P.138 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.141 SO4.4: 5 residues within 4Å: Chain A: K.147, G.148, S.149, D.150, H.151 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.148, A:H.151 Water bridges: A:D.150, A:D.150 SO4.8: 3 residues within 4Å: Chain A: P.138 Chain B: P.138, R.141 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.141 SO4.9: 5 residues within 4Å: Chain B: K.147, G.148, S.149, D.150, H.151 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.148, B:H.151 Water bridges: B:D.150, B:D.150

2 x ASC: ASCORBIC ACID(Post Translational Modification)

ASC.5: 10 residues within 4Å: Chain A: K.41, R.42, C.43, P.45, L.46, I.87, L.91, H.180, R.183 Ligands: HEM.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.41, A:L.46, A:H.180, A:R.183, A:R.183 Water bridges: A:A.178, A:H.180 ASC.10: 10 residues within 4Å: Chain B: K.41, R.42, C.43, P.45, L.46, I.87, L.91, H.180, R.183 Ligands: HEM.6 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.41, B:L.46, B:H.180, B:R.183, B:R.183 Water bridges: B:A.178, B:H.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kwon, H. et al., Visualizing the protons in a metalloenzyme electron proton transfer pathway. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-03-18

Peptides

Ascorbate peroxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Ascorbate peroxidase

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