SMTL ID : 2gvk.1

Crystal structure of a dye-decolorizing peroxidase (DyP) from Bacteroides thetaiotaomicron VPI-5482 at 1.6 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-hexamer

Ligands

18 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 4 residues within 4Å: Chain A: F.60, P.61, D.62, M.63 Ligand excluded by PLIP CL.2: 3 residues within 4Å: Chain A: F.92, S.93, R.274 Ligand excluded by PLIP CL.3: 4 residues within 4Å: Chain A: F.80, P.81, D.82, K.83 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain B: F.60, P.61, D.62, M.63 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain B: F.92, S.93, R.274 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain B: F.80, P.81, D.82, K.83 Ligand excluded by PLIP CL.25: 4 residues within 4Å: Chain C: F.60, P.61, D.62, M.63 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain C: F.92, S.93, R.274 Ligand excluded by PLIP CL.27: 4 residues within 4Å: Chain C: F.80, P.81, D.82, K.83 Ligand excluded by PLIP CL.37: 4 residues within 4Å: Chain D: F.60, P.61, D.62, M.63 Ligand excluded by PLIP CL.38: 3 residues within 4Å: Chain D: F.92, S.93, R.274 Ligand excluded by PLIP CL.39: 4 residues within 4Å: Chain D: F.80, P.81, D.82, K.83 Ligand excluded by PLIP CL.49: 4 residues within 4Å: Chain E: F.60, P.61, D.62, M.63 Ligand excluded by PLIP CL.50: 3 residues within 4Å: Chain E: F.92, S.93, R.274 Ligand excluded by PLIP CL.51: 4 residues within 4Å: Chain E: F.80, P.81, D.82, K.83 Ligand excluded by PLIP CL.61: 4 residues within 4Å: Chain F: F.60, P.61, D.62, M.63 Ligand excluded by PLIP CL.62: 3 residues within 4Å: Chain F: F.92, S.93, R.274 Ligand excluded by PLIP CL.63: 4 residues within 4Å: Chain F: F.80, P.81, D.82, K.83 Ligand excluded by PLIP

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

NA.4: 2 residues within 4Å: Chain A: P.36, D.37 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.37 NA.16: 2 residues within 4Å: Chain B: P.36, D.37 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.37 NA.28: 2 residues within 4Å: Chain C: P.36, D.37 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:P.36 NA.40: 2 residues within 4Å: Chain D: P.36, D.37 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.37, D:D.37 NA.52: 2 residues within 4Å: Chain E: P.36, D.37 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:P.36, E:D.37 NA.64: 2 residues within 4Å: Chain F: P.36, D.37 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:D.37, F:D.37

6 x UNL: UNKNOWN LIGAND

UNL.5: 10 residues within 4Å: Chain A: Q.21, R.146, Y.147, G.150, K.151, D.158, N.248, M.249, P.250 Chain B: N.58 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.21, A:Q.21, A:Q.21, A:R.146, A:Y.147, A:N.248, B:N.58 Water bridges: A:R.146, A:D.158 UNL.17: 10 residues within 4Å: Chain B: Q.21, R.146, Y.147, G.150, K.151, D.158, N.248, M.249, P.250 Chain C: N.58 9 PLIP interactions: 1 interactions with chain C, 8 interactions with chain B Hydrogen bonds: C:N.58, B:Q.21, B:R.146, B:Y.147, B:G.150, B:D.158, B:N.248 Water bridges: B:R.146, B:D.158 UNL.29: 10 residues within 4Å: Chain A: N.58 Chain C: Q.21, R.146, Y.147, G.150, K.151, D.158, N.248, M.249, P.250 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Q.21, C:Q.21, C:R.146, C:Y.147, C:D.158, C:N.248, A:N.58 Water bridges: C:R.146, C:D.158 UNL.41: 10 residues within 4Å: Chain D: Q.21, R.146, Y.147, G.150, K.151, D.158, N.248, M.249, P.250 Chain E: N.58 9 PLIP interactions: 2 interactions with chain E, 7 interactions with chain D Hydrogen bonds: E:N.58, E:N.58, D:Q.21, D:R.146, D:Y.147, D:G.150, D:N.248 Water bridges: D:R.146, D:N.248 UNL.53: 10 residues within 4Å: Chain E: Q.21, R.146, Y.147, G.150, K.151, D.158, N.248, M.249, P.250 Chain F: N.58 9 PLIP interactions: 8 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:Q.21, E:R.146, E:Y.147, E:G.150, E:D.158, E:N.248, F:N.58 Water bridges: E:R.146, E:N.248 UNL.65: 10 residues within 4Å: Chain D: N.58 Chain F: Q.21, R.146, Y.147, G.150, K.151, D.158, N.248, M.249, P.250 9 PLIP interactions: 8 interactions with chain F, 1 interactions with chain D Hydrogen bonds: F:Q.21, F:Q.21, F:R.146, F:Y.147, F:G.150, F:N.248, D:N.58 Water bridges: F:R.146, F:N.248

30 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 8 residues within 4Å: Chain A: V.29, T.105, P.106, V.139, V.190, T.300, G.301, T.302 Ligand excluded by PLIP EDO.7: 8 residues within 4Å: Chain A: Q.191, Y.193, H.232, R.246, N.248, F.263, M.280 Ligands: ACY.11 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: G.72, A.73, D.74, T.91, G.107, T.302 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: D.129, K.133 Chain E: S.255, K.256, G.257 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: H.171, F.172, L.242, S.268 Ligand excluded by PLIP EDO.18: 8 residues within 4Å: Chain B: V.29, T.105, P.106, V.139, V.190, T.300, G.301, T.302 Ligand excluded by PLIP EDO.19: 8 residues within 4Å: Chain B: Q.191, Y.193, H.232, R.246, N.248, F.263, M.280 Ligands: ACY.23 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain B: G.72, A.73, D.74, T.91, G.107, T.302 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain B: D.129, K.133 Chain D: S.255, K.256, G.257 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain B: H.171, F.172, L.242, S.268 Ligand excluded by PLIP EDO.30: 8 residues within 4Å: Chain C: V.29, T.105, P.106, V.139, V.190, T.300, G.301, T.302 Ligand excluded by PLIP EDO.31: 8 residues within 4Å: Chain C: Q.191, Y.193, H.232, R.246, N.248, F.263, M.280 Ligands: ACY.35 Ligand excluded by PLIP EDO.32: 6 residues within 4Å: Chain C: G.72, A.73, D.74, T.91, G.107, T.302 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain C: D.129, K.133 Chain F: S.255, K.256, G.257 Ligand excluded by PLIP EDO.34: 4 residues within 4Å: Chain C: H.171, F.172, L.242, S.268 Ligand excluded by PLIP EDO.42: 8 residues within 4Å: Chain D: V.29, T.105, P.106, V.139, V.190, T.300, G.301, T.302 Ligand excluded by PLIP EDO.43: 8 residues within 4Å: Chain D: Q.191, Y.193, H.232, R.246, N.248, F.263, M.280 Ligands: ACY.47 Ligand excluded by PLIP EDO.44: 6 residues within 4Å: Chain D: G.72, A.73, D.74, T.91, G.107, T.302 Ligand excluded by PLIP EDO.45: 5 residues within 4Å: Chain B: S.255, K.256, G.257 Chain D: D.129, K.133 Ligand excluded by PLIP EDO.46: 4 residues within 4Å: Chain D: H.171, F.172, L.242, S.268 Ligand excluded by PLIP EDO.54: 8 residues within 4Å: Chain E: V.29, T.105, P.106, V.139, V.190, T.300, G.301, T.302 Ligand excluded by PLIP EDO.55: 8 residues within 4Å: Chain E: Q.191, Y.193, H.232, R.246, N.248, F.263, M.280 Ligands: ACY.59 Ligand excluded by PLIP EDO.56: 6 residues within 4Å: Chain E: G.72, A.73, D.74, T.91, G.107, T.302 Ligand excluded by PLIP EDO.57: 5 residues within 4Å: Chain A: S.255, K.256, G.257 Chain E: D.129, K.133 Ligand excluded by PLIP EDO.58: 4 residues within 4Å: Chain E: H.171, F.172, L.242, S.268 Ligand excluded by PLIP EDO.66: 8 residues within 4Å: Chain F: V.29, T.105, P.106, V.139, V.190, T.300, G.301, T.302 Ligand excluded by PLIP EDO.67: 8 residues within 4Å: Chain F: Q.191, Y.193, H.232, R.246, N.248, F.263, M.280 Ligands: ACY.71 Ligand excluded by PLIP EDO.68: 6 residues within 4Å: Chain F: G.72, A.73, D.74, T.91, G.107, T.302 Ligand excluded by PLIP EDO.69: 5 residues within 4Å: Chain C: S.255, K.256, G.257 Chain F: D.129, K.133 Ligand excluded by PLIP EDO.70: 4 residues within 4Å: Chain F: H.171, F.172, L.242, S.268 Ligand excluded by PLIP

12 x ACY: ACETIC ACID(Non-functional Binders)

ACY.11: 6 residues within 4Å: Chain A: Y.193, H.195, N.248, L.292, S.296 Ligands: EDO.7 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.193, A:L.292 Hydrogen bonds: A:T.261, A:S.296, A:S.296 Salt bridges: A:H.195, A:H.232 ACY.12: 3 residues within 4Å: Chain A: D.149 Chain D: D.149 Ligands: ACY.48 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 interactions with chain D Water bridges: A:K.151, B:R.59 Salt bridges: A:K.151, D:K.151 ACY.23: 6 residues within 4Å: Chain B: Y.193, H.195, N.248, L.292, S.296 Ligands: EDO.19 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.193, B:L.292 Hydrogen bonds: B:T.261, B:S.296, B:S.296 Salt bridges: B:H.195, B:H.232 ACY.24: 3 residues within 4Å: Chain B: D.149 Chain F: D.149 Ligands: ACY.72 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain F, 1 interactions with chain C Water bridges: B:K.151, C:R.59 Salt bridges: B:K.151, F:K.151 ACY.35: 6 residues within 4Å: Chain C: Y.193, H.195, N.248, L.292, S.296 Ligands: EDO.31 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:Y.193, C:L.292 Hydrogen bonds: C:T.261, C:S.296, C:S.296 Salt bridges: C:H.195, C:H.232 ACY.36: 3 residues within 4Å: Chain C: D.149 Chain E: D.149 Ligands: ACY.60 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C, 1 interactions with chain E Water bridges: A:R.59, C:K.151 Salt bridges: C:K.151, E:K.151 ACY.47: 6 residues within 4Å: Chain D: Y.193, H.195, N.248, L.292, S.296 Ligands: EDO.43 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:Y.193, D:L.292 Hydrogen bonds: D:S.296, D:S.296 Salt bridges: D:H.195, D:H.232 ACY.48: 3 residues within 4Å: Chain A: D.149 Chain D: D.149 Ligands: ACY.12 4 PLIP interactions: 1 interactions with chain E, 2 interactions with chain D, 1 interactions with chain A Water bridges: E:R.59, D:K.151 Salt bridges: D:K.151, A:K.151 ACY.59: 6 residues within 4Å: Chain E: Y.193, H.195, N.248, L.292, S.296 Ligands: EDO.55 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:Y.193, E:L.292 Hydrogen bonds: E:S.296, E:S.296 Salt bridges: E:H.195, E:H.232 ACY.60: 3 residues within 4Å: Chain C: D.149 Chain E: D.149 Ligands: ACY.36 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain F, 2 interactions with chain E Salt bridges: C:K.151, E:K.151 Water bridges: F:R.59, E:K.151 ACY.71: 6 residues within 4Å: Chain F: Y.193, H.195, N.248, L.292, S.296 Ligands: EDO.67 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:Y.193, F:L.292 Hydrogen bonds: F:S.296, F:S.296 Salt bridges: F:H.195, F:H.232 ACY.72: 3 residues within 4Å: Chain B: D.149 Chain F: D.149 Ligands: ACY.24 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B, 2 interactions with chain F Water bridges: D:R.59, F:K.151 Salt bridges: B:K.151, F:K.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zubieta, C. et al., Crystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif. Proteins (2007)

Release Date

2006-05-16

Peptides

Heme peroxidase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Heme peroxidase