SMTL ID : 4uzi.1

Crystal Structure of AauDyP Complexed with Imidazole

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: P.181, Q.276, N.280, T.317, P.318 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.317

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG-BMA.2: 5 residues within 4Å: Chain B: P.181, Q.276, N.280, T.317, P.318 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.317

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

HEM.3: 27 residues within 4Å: Chain A: E.160, F.162, F.164, L.165, D.166, G.167, I.168, A.169, L.217, Q.219, V.251, R.253, H.302, I.303, T.306, R.307, R.309, R.330, L.355, F.357, F.368, L.371, Q.372, I.395, I.396, V.424 Ligands: IMD.6 35 PLIP interactions: 35 interactions with chain A, Hydrophobic interactions: A:F.162, A:F.164, A:A.169, A:L.217, A:Q.219, A:V.251, A:I.303, A:I.303, A:T.306, A:L.355, A:L.355, A:F.357, A:F.357, A:F.368, A:L.371, A:I.395, A:I.396, A:I.396, A:V.424 Hydrogen bonds: A:D.166, A:G.167, A:I.168, A:A.169, A:I.303 Water bridges: A:R.253, A:R.307, A:R.307, A:R.309, A:R.309 Salt bridges: A:R.253, A:R.307, A:R.309, A:R.330 pi-Cation interactions: A:R.330 Metal complexes: A:H.302 HEM.18: 27 residues within 4Å: Chain B: E.160, F.162, F.164, L.165, D.166, G.167, I.168, A.169, L.217, Q.219, V.251, R.253, H.302, I.303, T.306, R.307, R.309, R.330, L.355, F.357, F.368, L.371, Q.372, I.395, I.396, V.424 Ligands: IMD.21 33 PLIP interactions: 33 interactions with chain B, Hydrophobic interactions: B:F.162, B:F.164, B:L.217, B:Q.219, B:V.251, B:T.306, B:R.307, B:L.355, B:L.355, B:F.357, B:F.357, B:F.368, B:L.371, B:I.395, B:I.396, B:V.424, B:V.424 Hydrogen bonds: B:D.166, B:D.166, B:G.167, B:I.168, B:A.169, B:I.303 Water bridges: B:R.253, B:R.307, B:R.309, B:R.309 Salt bridges: B:R.253, B:R.307, B:R.309, B:R.330 pi-Cation interactions: B:R.330 Metal complexes: B:H.302

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.4: 6 residues within 4Å: Chain A: K.226, D.230, A.345, N.347 Ligands: ACT.14, OXD.16 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.226, A:D.230, A:A.345, A:N.347 NAG.5: 3 residues within 4Å: Chain A: N.413, S.415, A.416 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.413 NAG.19: 4 residues within 4Å: Chain B: D.230, A.345, S.346, N.347 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.230, B:A.345, B:N.347 NAG.20: 3 residues within 4Å: Chain B: N.413, S.415, A.416 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.413, B:N.413

4 x IMD: IMIDAZOLE(Non-covalent)

IMD.6: 5 residues within 4Å: Chain A: D.166, R.330, L.355, F.357 Ligands: HEM.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.330 pi-Cation interactions: A:R.330 IMD.7: 8 residues within 4Å: Chain A: L.12, V.13, G.14, Q.170, M.329, R.330, S.331 Ligands: MRD.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.170 Water bridges: A:S.331 IMD.21: 5 residues within 4Å: Chain B: D.166, R.330, L.355, F.357 Ligands: HEM.18 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.330 Water bridges: B:G.332 pi-Cation interactions: B:R.330 IMD.22: 7 residues within 4Å: Chain B: L.12, V.13, G.14, Q.170, M.329, R.330, S.331 2 PLIP interactions: 2 interactions with chain B Water bridges: B:V.13, B:Q.170

1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.8: 9 residues within 4Å: Chain A: I.151, G.158, D.166, G.167, Q.170, R.330, S.331, G.332 Ligands: IMD.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.151 Hydrogen bonds: A:G.158, A:R.330

7 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.9: 2 residues within 4Å: Chain A: N.400, Q.402 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.400, A:Q.402 Hydrogen bonds: A:N.400 Water bridges: A:Q.402 MPD.10: 2 residues within 4Å: Chain A: K.97, N.399 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.97, A:N.400 MPD.23: 8 residues within 4Å: Chain B: G.158, D.166, G.167, Q.170, R.330, S.331, G.332, I.333 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.330 Water bridges: B:G.158 MPD.24: 6 residues within 4Å: Chain A: S.341 Chain B: D.40, V.44, Q.129, S.132, T.136 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:S.341, B:Q.129, B:S.132, B:S.132 Water bridges: A:A.342 Hydrophobic interactions: B:V.44 MPD.25: 5 residues within 4Å: Chain B: N.174, I.185, V.186, D.187, L.321 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:N.174, B:L.321 Hydrogen bonds: B:I.185, B:D.187 Water bridges: B:N.174 MPD.26: 4 residues within 4Å: Chain B: T.4, V.48, F.176 Ligands: ACT.30 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.48, B:F.176 Hydrogen bonds: B:T.4 Water bridges: B:F.176 MPD.27: 8 residues within 4Å: Chain A: K.19, T.122, T.123, D.124 Chain B: K.19, T.122, T.123, D.124 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:T.123, A:D.124, B:T.123 Hydrogen bonds: A:T.123, A:D.124, A:D.124, B:T.123, B:T.123, B:D.124

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

FMT.11: 5 residues within 4Å: Chain A: L.290, A.310, G.313, G.314, L.316 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.313, A:G.314

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.12: 5 residues within 4Å: Chain A: Q.106, K.143, L.144, Y.145, S.146 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.106, A:S.146 Salt bridges: A:K.143 EPE.28: 4 residues within 4Å: Chain B: K.143, Y.145, S.146, E.352 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.146, B:S.146, B:E.352 Salt bridges: B:K.143

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.13: 5 residues within 4Å: Chain A: Y.23, E.134, I.141, S.142, K.143 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.134 Hydrogen bonds: A:K.143 ACT.14: 3 residues within 4Å: Chain A: D.230, L.239 Ligands: NAG.4 No protein-ligand interaction detected (PLIP) ACT.15: 4 residues within 4Å: Chain A: D.40, Q.129, S.132, I.133 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.132, A:T.136 ACT.29: 3 residues within 4Å: Chain B: L.229, S.344, N.347 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.344 ACT.30: 2 residues within 4Å: Chain B: N.177 Ligands: MPD.26 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.177 Water bridges: B:T.178 ACT.33: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.175

1 x OXD: OXALIC ACID(Non-covalent)

OXD.16: 4 residues within 4Å: Chain A: S.344, A.345, N.347 Ligands: NAG.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.344, A:S.344

2 x K: POTASSIUM ION(Non-covalent)

K.17: 4 residues within 4Å: Chain A: D.82, Q.363, L.364, S.365 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.82, H2O.3, H2O.11 K.31: 4 residues within 4Å: Chain B: D.82, Q.363, L.364, S.365 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.82, H2O.15

1 x GOA: GLYCOLIC ACID(Non-functional Binders)

GOA.32: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Strittmatter, E. et al., The Toolbox of Auricularia Auricula-Judae Dye-Decolorizing Peroxidase - Identification of Three New Potential Substrate-Interaction Sites. Arch.Biochem.Biophys. (2015)

Release Date

2015-01-14

Peptides

DYE-DECOLORIZING PEROXIDASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DYE-DECOLORIZING PEROXIDASE

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