SMTL ID : 3qns.1

DyPB from Rhodococcus jostii RHA1, crystal form 2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-hexamer

Ligands

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

HEM.1: 25 residues within 4Å: Chain A: D.150, L.152, F.154, V.155, D.156, G.157, T.158, E.159, Q.188, Y.190, H.192, I.209, R.211, H.229, V.230, N.233, T.234, R.247, F.264, T.274, M.277, L.278, M.281, V.293, S.297 25 PLIP interactions: 24 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:L.152, A:F.154, A:Y.190, A:Y.190, A:I.209, A:N.233, A:F.264, A:F.264, A:T.274, A:M.277, A:L.278, A:L.278, A:V.293 Hydrogen bonds: A:G.157, A:T.158, A:E.159 Water bridges: A:E.159, A:E.159, A:R.211, A:E.242, A:D.244 Salt bridges: A:R.247 pi-Cation interactions: A:R.247 Metal complexes: A:H.229, H2O.6 HEM.9: 25 residues within 4Å: Chain B: D.150, L.152, F.154, V.155, D.156, G.157, T.158, E.159, Q.188, Y.190, H.192, I.209, R.211, H.229, V.230, N.233, T.234, R.247, F.264, T.274, M.277, L.278, M.281, V.293, S.297 25 PLIP interactions: 24 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:L.152, B:F.154, B:Y.190, B:Y.190, B:I.209, B:N.233, B:F.264, B:F.264, B:T.274, B:M.277, B:L.278, B:L.278, B:V.293 Hydrogen bonds: B:G.157, B:T.158, B:E.159 Water bridges: B:E.159, B:E.159, B:R.211, B:E.242, B:D.244 Salt bridges: B:R.247 pi-Cation interactions: B:R.247 Metal complexes: B:H.229, H2O.22 HEM.17: 25 residues within 4Å: Chain C: D.150, L.152, F.154, V.155, D.156, G.157, T.158, E.159, Q.188, Y.190, H.192, I.209, R.211, H.229, V.230, N.233, T.234, R.247, F.264, T.274, M.277, L.278, M.281, V.293, S.297 25 PLIP interactions: 24 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: C:L.152, C:F.154, C:Y.190, C:Y.190, C:I.209, C:N.233, C:F.264, C:F.264, C:T.274, C:M.277, C:L.278, C:L.278, C:V.293 Hydrogen bonds: C:G.157, C:T.158, C:E.159 Water bridges: C:E.159, C:E.159, C:R.211, C:E.242, C:D.244 Salt bridges: C:R.247 pi-Cation interactions: C:R.247 Metal complexes: C:H.229, H2O.38 HEM.25: 25 residues within 4Å: Chain D: D.150, L.152, F.154, V.155, D.156, G.157, T.158, E.159, Q.188, Y.190, H.192, I.209, R.211, H.229, V.230, N.233, T.234, R.247, F.264, T.274, M.277, L.278, M.281, V.293, S.297 25 PLIP interactions: 24 interactions with chain D, 1 Ligand-Water interactions Hydrophobic interactions: D:L.152, D:F.154, D:Y.190, D:Y.190, D:I.209, D:N.233, D:F.264, D:F.264, D:T.274, D:M.277, D:L.278, D:L.278, D:V.293 Hydrogen bonds: D:G.157, D:T.158, D:E.159 Water bridges: D:R.211, D:T.234, D:T.234, D:E.242, D:D.244 Salt bridges: D:R.247 pi-Cation interactions: D:R.247 Metal complexes: D:H.229, H2O.54 HEM.33: 25 residues within 4Å: Chain E: D.150, L.152, F.154, V.155, D.156, G.157, T.158, E.159, Q.188, Y.190, H.192, I.209, R.211, H.229, V.230, N.233, T.234, R.247, F.264, T.274, M.277, L.278, M.281, V.293, S.297 25 PLIP interactions: 24 interactions with chain E, 1 Ligand-Water interactions Hydrophobic interactions: E:L.152, E:F.154, E:Y.190, E:Y.190, E:I.209, E:N.233, E:F.264, E:F.264, E:T.274, E:M.277, E:L.278, E:L.278, E:V.293 Hydrogen bonds: E:G.157, E:T.158, E:E.159 Water bridges: E:R.211, E:T.234, E:T.234, E:E.242, E:D.244 Salt bridges: E:R.247 pi-Cation interactions: E:R.247 Metal complexes: E:H.229, H2O.70 HEM.41: 25 residues within 4Å: Chain F: D.150, L.152, F.154, V.155, D.156, G.157, T.158, E.159, Q.188, Y.190, H.192, I.209, R.211, H.229, V.230, N.233, T.234, R.247, F.264, T.274, M.277, L.278, M.281, V.293, S.297 25 PLIP interactions: 24 interactions with chain F, 1 Ligand-Water interactions Hydrophobic interactions: F:L.152, F:F.154, F:Y.190, F:Y.190, F:I.209, F:N.233, F:F.264, F:F.264, F:T.274, F:M.277, F:L.278, F:L.278, F:V.293 Hydrogen bonds: F:G.157, F:T.158, F:E.159 Water bridges: F:R.211, F:T.234, F:T.234, F:E.242, F:D.244 Salt bridges: F:R.247 pi-Cation interactions: F:R.247 Metal complexes: F:H.229, H2O.85

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

SO4.2: 5 residues within 4Å: Chain A: K.116, H.141 Chain F: K.116, G.253 Ligands: SO4.42 12 PLIP interactions: 5 interactions with chain F, 7 interactions with chain A Water bridges: F:K.116, F:K.116, F:K.116, F:K.116, A:K.116, A:K.116, A:K.116, A:K.116, A:H.141 Salt bridges: F:K.116, A:K.116, A:H.141 SO4.3: 6 residues within 4Å: Chain A: R.58, E.59, L.60, R.115 Chain B: R.144 Ligands: SO4.35 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:L.60 Water bridges: A:R.115, A:R.115 Salt bridges: A:R.115, B:R.144 SO4.10: 5 residues within 4Å: Chain B: K.116, H.141 Chain E: K.116, G.253 Ligands: SO4.34 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain E Water bridges: B:K.116, B:K.116, B:K.116, B:K.116, B:H.141, E:K.116, E:K.116, E:K.116 Salt bridges: B:K.116, B:H.141, E:K.116 SO4.11: 6 residues within 4Å: Chain B: R.58, E.59, L.60, R.115 Chain C: R.144 Ligands: SO4.27 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:L.60 Water bridges: B:R.115, B:R.115 Salt bridges: B:R.115, C:R.144 SO4.18: 5 residues within 4Å: Chain C: K.116, H.141 Chain D: K.116, G.253 Ligands: SO4.26 11 PLIP interactions: 7 interactions with chain C, 4 interactions with chain D Water bridges: C:K.116, C:K.116, C:K.116, C:K.116, C:H.141, D:K.116, D:K.116, D:K.116 Salt bridges: C:K.116, C:H.141, D:K.116 SO4.19: 6 residues within 4Å: Chain A: R.144 Chain C: R.58, E.59, L.60, R.115 Ligands: SO4.43 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:L.60 Water bridges: C:R.115, C:R.115 Salt bridges: C:R.115, A:R.144 SO4.26: 5 residues within 4Å: Chain C: K.116, G.253 Chain D: K.116, H.141 Ligands: SO4.18 11 PLIP interactions: 7 interactions with chain D, 4 interactions with chain C Water bridges: D:K.116, D:K.116, D:K.116, D:K.116, D:H.141, C:K.116, C:K.116, C:K.116 Salt bridges: D:K.116, D:H.141, C:K.116 SO4.27: 6 residues within 4Å: Chain D: R.58, E.59, L.60, R.115 Chain E: R.144 Ligands: SO4.11 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:L.60 Water bridges: D:R.115, D:R.115 Salt bridges: D:R.115, E:R.144 SO4.34: 5 residues within 4Å: Chain B: K.116, G.253 Chain E: K.116, H.141 Ligands: SO4.10 11 PLIP interactions: 4 interactions with chain B, 7 interactions with chain E Water bridges: B:K.116, B:K.116, B:K.116, E:K.116, E:K.116, E:K.116, E:K.116, E:H.141 Salt bridges: B:K.116, E:K.116, E:H.141 SO4.35: 6 residues within 4Å: Chain E: R.58, E.59, L.60, R.115 Chain F: R.144 Ligands: SO4.3 5 PLIP interactions: 1 interactions with chain F, 4 interactions with chain E Salt bridges: F:R.144, E:R.115 Hydrogen bonds: E:L.60 Water bridges: E:R.115, E:R.115 SO4.42: 5 residues within 4Å: Chain A: K.116, G.253 Chain F: K.116, H.141 Ligands: SO4.2 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain F Water bridges: A:K.116, A:K.116, A:K.116, A:H.141, F:K.116, F:K.116, F:K.116, F:K.116, F:H.141 Salt bridges: A:K.116, F:K.116, F:H.141 SO4.43: 6 residues within 4Å: Chain D: R.144 Chain F: R.58, E.59, L.60, R.115 Ligands: SO4.19 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain D Hydrogen bonds: F:L.60 Water bridges: F:R.115, F:R.115 Salt bridges: F:R.115, D:R.144

30 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 1 residues within 4Å: Chain A: P.287 Ligand excluded by PLIP GOL.5: 10 residues within 4Å: Chain A: L.214, E.215 Chain C: R.124 Chain D: L.151, L.152, G.153, M.194, W.197, N.198, K.213 Ligand excluded by PLIP GOL.6: 3 residues within 4Å: Chain A: P.225, S.226, N.227 Ligand excluded by PLIP GOL.7: 6 residues within 4Å: Chain A: H.192, D.193, M.194, S.195, A.258, Y.260 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain A: N.227, G.288, N.289, Y.290 Ligand excluded by PLIP GOL.12: 1 residues within 4Å: Chain B: P.287 Ligand excluded by PLIP GOL.13: 10 residues within 4Å: Chain A: R.124 Chain B: L.214, E.215 Chain F: L.151, L.152, G.153, M.194, W.197, N.198, K.213 Ligand excluded by PLIP GOL.14: 3 residues within 4Å: Chain B: P.225, S.226, N.227 Ligand excluded by PLIP GOL.15: 6 residues within 4Å: Chain B: H.192, D.193, M.194, S.195, A.258, Y.260 Ligand excluded by PLIP GOL.16: 4 residues within 4Å: Chain B: N.227, G.288, N.289, Y.290 Ligand excluded by PLIP GOL.20: 1 residues within 4Å: Chain C: P.287 Ligand excluded by PLIP GOL.21: 10 residues within 4Å: Chain B: R.124 Chain C: L.214, E.215 Chain E: L.151, L.152, G.153, M.194, W.197, N.198, K.213 Ligand excluded by PLIP GOL.22: 3 residues within 4Å: Chain C: P.225, S.226, N.227 Ligand excluded by PLIP GOL.23: 6 residues within 4Å: Chain C: H.192, D.193, M.194, S.195, A.258, Y.260 Ligand excluded by PLIP GOL.24: 4 residues within 4Å: Chain C: N.227, G.288, N.289, Y.290 Ligand excluded by PLIP GOL.28: 1 residues within 4Å: Chain D: P.287 Ligand excluded by PLIP GOL.29: 10 residues within 4Å: Chain A: L.151, L.152, G.153, M.194, W.197, N.198, K.213 Chain D: L.214, E.215 Chain F: R.124 Ligand excluded by PLIP GOL.30: 3 residues within 4Å: Chain D: P.225, S.226, N.227 Ligand excluded by PLIP GOL.31: 6 residues within 4Å: Chain D: H.192, D.193, M.194, S.195, A.258, Y.260 Ligand excluded by PLIP GOL.32: 4 residues within 4Å: Chain D: N.227, G.288, N.289, Y.290 Ligand excluded by PLIP GOL.36: 1 residues within 4Å: Chain E: P.287 Ligand excluded by PLIP GOL.37: 10 residues within 4Å: Chain C: L.151, L.152, G.153, M.194, W.197, N.198, K.213 Chain D: R.124 Chain E: L.214, E.215 Ligand excluded by PLIP GOL.38: 3 residues within 4Å: Chain E: P.225, S.226, N.227 Ligand excluded by PLIP GOL.39: 6 residues within 4Å: Chain E: H.192, D.193, M.194, S.195, A.258, Y.260 Ligand excluded by PLIP GOL.40: 4 residues within 4Å: Chain E: N.227, G.288, N.289, Y.290 Ligand excluded by PLIP GOL.44: 1 residues within 4Å: Chain F: P.287 Ligand excluded by PLIP GOL.45: 10 residues within 4Å: Chain B: L.151, L.152, G.153, M.194, W.197, N.198, K.213 Chain E: R.124 Chain F: L.214, E.215 Ligand excluded by PLIP GOL.46: 3 residues within 4Å: Chain F: P.225, S.226, N.227 Ligand excluded by PLIP GOL.47: 6 residues within 4Å: Chain F: H.192, D.193, M.194, S.195, A.258, Y.260 Ligand excluded by PLIP GOL.48: 4 residues within 4Å: Chain F: N.227, G.288, N.289, Y.290 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roberts, J.N. et al., Characterization of dye-decolorizing peroxidases from Rhodococcus jostii RHA1. Biochemistry (2011)

Release Date

2011-04-27

Peptides

DyP Peroxidase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

DyP Peroxidase

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