SMTL ID : 7qzg.1

SFX structure of dye-type peroxidase DtpB N245A variant in the ferric state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-hexamer

Ligands

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

HEM.1: 22 residues within 4Å: Chain A: D.146, F.150, V.151, D.152, G.153, T.154, E.155, Q.184, Y.186, R.207, H.225, V.226, T.229, S.230, R.243, T.258, F.260, M.273, L.274, M.277, I.289, S.293 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:F.150, A:Y.186, A:Y.186, A:T.229, A:T.258, A:F.260, A:F.260, A:M.273, A:L.274, A:I.289 Hydrogen bonds: A:G.153, A:T.154, A:E.155 Water bridges: A:E.155, A:R.207, A:R.207 Salt bridges: A:R.243 pi-Stacking: A:F.260 pi-Cation interactions: A:R.243 Metal complexes: A:H.225 HEM.3: 23 residues within 4Å: Chain B: D.146, L.148, F.150, V.151, D.152, G.153, T.154, E.155, Q.184, Y.186, H.188, R.207, H.225, T.229, S.230, R.243, T.258, F.260, T.270, M.273, L.274, M.277, I.289 20 PLIP interactions: 20 interactions with chain B, Hydrophobic interactions: B:L.148, B:F.150, B:Y.186, B:Y.186, B:T.229, B:T.258, B:F.260, B:F.260, B:F.260, B:T.270, B:M.273, B:L.274, B:I.289 Hydrogen bonds: B:G.153, B:T.154, B:E.155 Water bridges: B:R.207, B:R.207 Salt bridges: B:R.243 Metal complexes: B:H.225 HEM.4: 23 residues within 4Å: Chain C: D.146, L.148, F.150, V.151, D.152, G.153, T.154, E.155, Q.184, Y.186, H.188, R.207, H.225, T.229, S.230, R.243, T.258, F.260, M.273, L.274, M.277, I.289, S.293 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:L.148, C:F.150, C:Y.186, C:Y.186, C:T.229, C:F.260, C:F.260, C:M.273, C:I.289 Hydrogen bonds: C:G.153, C:T.154, C:E.155 Water bridges: C:T.229 Salt bridges: C:R.243 pi-Stacking: C:F.260 pi-Cation interactions: C:R.243 Metal complexes: C:H.225 HEM.5: 22 residues within 4Å: Chain D: D.146, F.150, V.151, D.152, G.153, T.154, E.155, Q.184, Y.186, H.188, R.207, H.225, V.226, T.229, R.243, T.258, F.260, T.270, M.273, M.277, I.289, S.293 17 PLIP interactions: 17 interactions with chain D, Hydrophobic interactions: D:F.150, D:Y.186, D:Y.186, D:T.229, D:F.260, D:F.260, D:F.260, D:T.270, D:M.273, D:I.289 Hydrogen bonds: D:G.153, D:T.154, D:E.155 Water bridges: D:R.207, D:T.229 Salt bridges: D:R.243 Metal complexes: D:H.225 HEM.7: 21 residues within 4Å: Chain E: D.146, F.150, V.151, D.152, G.153, T.154, E.155, Q.184, Y.186, R.207, H.225, T.229, S.230, R.243, T.258, F.260, T.270, M.273, L.274, M.277, I.289 19 PLIP interactions: 19 interactions with chain E, Hydrophobic interactions: E:F.150, E:Y.186, E:T.229, E:T.258, E:F.260, E:F.260, E:F.260, E:T.270, E:L.274, E:I.289 Hydrogen bonds: E:D.152, E:D.152, E:G.153, E:T.154, E:E.155 Water bridges: E:R.207 Salt bridges: E:R.243 pi-Cation interactions: E:R.243 Metal complexes: E:H.225 HEM.8: 24 residues within 4Å: Chain F: D.146, F.150, V.151, D.152, G.153, T.154, E.155, Q.184, Y.186, H.188, R.207, H.225, V.226, T.229, S.230, R.243, T.258, F.260, T.270, M.273, L.274, M.277, I.289, S.293 21 PLIP interactions: 21 interactions with chain F, Hydrophobic interactions: F:F.150, F:Y.186, F:Y.186, F:T.229, F:F.260, F:F.260, F:F.260, F:T.270, F:M.273, F:I.289 Hydrogen bonds: F:G.153, F:T.154, F:E.155 Water bridges: F:E.155, F:E.155, F:R.207, F:R.207 Salt bridges: F:R.243 pi-Stacking: F:F.260 pi-Cation interactions: F:R.243 Metal complexes: F:H.225

2 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 3 residues within 4Å: Chain A: D.191, E.254 Chain C: R.127 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.191, H2O.1, H2O.1, H2O.2 MG.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lucic, M. et al., Serial Femtosecond Crystallography Reveals the Role of Water in the One- or Two-Electron Redox Chemistry of Compound I in the Catalytic Cycle of the B-Type Dye-Decolorizing Peroxidase DtpB. Acs Catalysis (2022)

Release Date

2022-12-07

Peptides

Dyp-type peroxidase family: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Dyp-type peroxidase family