SMTL ID : 3qnr.1

DyPB from Rhodococcus jostii RHA1, crystal form 1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 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, R.247, T.262, F.264, T.274, M.277, L.278, M.281, V.293, S.297 26 PLIP interactions: 25 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:L.152, A:F.154, A:Y.190, 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:R.211, A:R.211, A:N.233, A:D.244 Salt bridges: A:R.247 pi-Stacking: A:H.229 pi-Cation interactions: A:R.247 Metal complexes: A:H.229, H2O.7 HEM.4: 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, I.245, R.247, F.264, T.274, M.277, L.278, M.281, V.293, S.297 24 PLIP interactions: 23 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:L.152, B:F.154, B:Y.190, B:Y.190, B:Y.190, B:I.209, B:N.233, B:I.245, 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:R.211 Salt bridges: B:R.247 pi-Stacking: B:H.229 pi-Cation interactions: B:R.247 Metal complexes: B:H.229, H2O.9 HEM.7: 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, I.245, R.247, T.262, F.264, T.274, M.277, L.278, M.281, S.297 23 PLIP interactions: 22 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: C:L.152, C:F.154, C:Y.190, C:Y.190, C:Y.190, C:I.209, C:N.233, C:I.245, C:F.264, C:F.264, C:T.274, C:M.277, C:L.278, C:L.278 Hydrogen bonds: C:G.157, C:T.158, C:E.159 Water bridges: C:R.211 Salt bridges: C:R.247 pi-Stacking: C:H.229 pi-Cation interactions: C:R.247 Metal complexes: C:H.229, H2O.17 HEM.9: 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, R.247, T.262, F.264, T.274, M.277, L.278, M.281, V.293, S.297 28 PLIP interactions: 27 interactions with chain D, 1 Ligand-Water interactions Hydrophobic interactions: D:L.152, D:F.154, D:Y.190, 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:E.159, D:R.211, D:R.211, D:N.233, D:E.242, D:D.244 Salt bridges: D:R.247 pi-Stacking: D:H.229 pi-Cation interactions: D:R.247 Metal complexes: D:H.229, H2O.24 HEM.12: 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, I.245, R.247, F.264, T.274, M.277, L.278, M.281, V.293, S.297 24 PLIP interactions: 23 interactions with chain E, 1 Ligand-Water interactions Hydrophobic interactions: E:L.152, E:F.154, E:Y.190, E:Y.190, E:Y.190, E:I.209, E:N.233, E:I.245, 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 Salt bridges: E:R.247 pi-Stacking: E:H.229 pi-Cation interactions: E:R.247 Metal complexes: E:H.229, H2O.26 HEM.15: 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, I.245, R.247, T.262, F.264, T.274, M.277, L.278, M.281, S.297 23 PLIP interactions: 22 interactions with chain F, 1 Ligand-Water interactions Hydrophobic interactions: F:L.152, F:F.154, F:Y.190, F:Y.190, F:Y.190, F:I.209, F:N.233, F:I.245, F:F.264, F:F.264, F:T.274, F:M.277, F:L.278, F:L.278 Hydrogen bonds: F:G.157, F:T.158, F:E.159 Water bridges: F:R.211 Salt bridges: F:R.247 pi-Stacking: F:H.229 pi-Cation interactions: F:R.247 Metal complexes: F:H.229, H2O.35

6 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 6 residues within 4Å: Chain A: R.58, E.121 Chain B: Y.145, F.146 Chain C: L.214, E.215 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.58, A:R.58, A:E.121 FMT.5: 5 residues within 4Å: Chain A: R.115, K.116 Chain B: A.114, R.115, K.116 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.116, A:K.116 FMT.8: 5 residues within 4Å: Chain C: R.144, Y.145, S.148, R.149, N.249 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.145, C:Y.145 FMT.10: 6 residues within 4Å: Chain D: R.58, E.121 Chain E: Y.145, F.146 Chain F: L.214, E.215 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:R.58, D:R.58, D:E.121, E:Y.145 FMT.13: 5 residues within 4Å: Chain D: R.115, K.116 Chain E: A.114, R.115, K.116 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:K.116, E:K.116 FMT.16: 5 residues within 4Å: Chain F: R.144, Y.145, S.148, R.149, N.249 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Y.145, F:Y.145

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: N.227, G.288, N.289, Y.290, R.292, D.295 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.227, A:Y.290, A:Y.290, A:R.292 Water bridges: A:Y.290 GOL.6: 5 residues within 4Å: Chain B: L.191, H.192, D.193, F.296, T.298 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.298, B:T.298 Water bridges: B:H.192, B:D.193, B:M.194, B:S.297 GOL.11: 6 residues within 4Å: Chain D: N.227, G.288, N.289, Y.290, R.292, D.295 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.227, D:Y.290, D:Y.290, D:R.292 GOL.14: 5 residues within 4Å: Chain E: L.191, H.192, D.193, F.296, T.298 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:T.298, E:T.298, E:T.298 Water bridges: E:H.192, E:D.193, E:M.194, E:S.297

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
B

C
C

D
A

E
B

F
C

DyP Peroxidase

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