SMTL ID : 4g2c.1 (1 other biounit)

DyP2 from Amycolatopsis sp. ATCC 39116

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

monomer

Ligands

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

HEM.1: 25 residues within 4Å: Chain A: E.213, Y.217, V.218, D.219, G.220, R.221, S.222, L.276, Q.278, V.309, R.311, H.350, I.351, T.354, N.355, R.357, R.375, L.403, F.405, F.416, T.419, Q.420, V.443, I.444, V.474 28 PLIP interactions: 28 interactions with chain A, Hydrophobic interactions: A:E.213, A:Y.217, A:L.276, A:Q.278, A:V.309, A:I.351, A:I.351, A:N.355, A:L.403, A:L.403, A:F.405, A:F.405, A:F.416, A:T.419, A:V.443, A:I.444, A:I.444, A:V.474 Hydrogen bonds: A:G.220, A:R.221, A:S.222, A:S.222, A:N.355 Salt bridges: A:R.311, A:R.357, A:R.375 pi-Cation interactions: A:R.375 Metal complexes: A:H.350

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 4 residues within 4Å: Chain A: Y.217, K.284, E.287, E.313 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.287, A:E.313, H2O.3

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

ACT.3: 7 residues within 4Å: Chain A: E.251, Q.252, K.370, S.410, N.411, N.414, Q.415 Ligand excluded by PLIP ACT.4: 5 residues within 4Å: Chain A: D.239, S.326, P.329, V.330, G.331 Ligand excluded by PLIP ACT.5: 6 residues within 4Å: Chain A: V.231, R.235, V.241, D.245, S.247 Ligands: ACT.27 Ligand excluded by PLIP ACT.6: 4 residues within 4Å: Chain A: N.242, D.243, S.335, D.337 Ligand excluded by PLIP ACT.7: 8 residues within 4Å: Chain A: G.342, P.346, F.347, H.348, K.453, Y.454, A.455 Ligands: ACT.8 Ligand excluded by PLIP ACT.8: 6 residues within 4Å: Chain A: F.347, D.434, S.436, Q.437, P.438 Ligands: ACT.7 Ligand excluded by PLIP ACT.9: 5 residues within 4Å: Chain A: D.337, S.338, D.339, K.340, L.341 Ligand excluded by PLIP ACT.10: 7 residues within 4Å: Chain A: A.61, R.64, G.220, Q.223, R.376 Ligands: ACT.13, ACT.22 Ligand excluded by PLIP ACT.11: 7 residues within 4Å: Chain A: K.147, G.413, N.414, E.417, F.418, Q.421, I.422 Ligand excluded by PLIP ACT.12: 3 residues within 4Å: Chain A: D.232, R.235, D.236 Ligand excluded by PLIP ACT.13: 7 residues within 4Å: Chain A: D.219, G.220, Q.223, R.375, G.377, L.403 Ligands: ACT.10 Ligand excluded by PLIP ACT.14: 3 residues within 4Å: Chain A: T.82, N.85, L.493 Ligand excluded by PLIP ACT.15: 2 residues within 4Å: Chain A: R.281, K.399 Ligand excluded by PLIP ACT.16: 1 residues within 4Å: Chain A: A.139 Ligand excluded by PLIP ACT.17: 7 residues within 4Å: Chain A: V.63, H.97, E.100, V.101, V.110, G.111, T.112 Ligand excluded by PLIP ACT.18: 7 residues within 4Å: Chain A: R.66, L.67, T.68, A.175, V.178, S.200, G.201 Ligand excluded by PLIP ACT.19: 2 residues within 4Å: Chain A: A.125, T.126 Ligand excluded by PLIP ACT.20: 7 residues within 4Å: Chain A: S.35, T.36, T.37, S.247, A.248, P.249 Ligands: ACT.27 Ligand excluded by PLIP ACT.21: 7 residues within 4Å: Chain A: P.224, P.246, S.247, A.248, Q.252, R.369, L.372 Ligand excluded by PLIP ACT.22: 9 residues within 4Å: Chain A: L.59, K.60, A.61, Q.223, P.224, L.225, D.230, R.376 Ligands: ACT.10 Ligand excluded by PLIP ACT.23: 7 residues within 4Å: Chain A: L.440, R.449, A.450, P.451, Q.452, P.469, I.470 Ligand excluded by PLIP ACT.24: 4 residues within 4Å: Chain A: P.135, T.138, A.139 Ligands: ACT.25 Ligand excluded by PLIP ACT.25: 9 residues within 4Å: Chain A: S.136, A.139, G.140, A.143, A.144, K.147, E.417, Y.481 Ligands: ACT.24 Ligand excluded by PLIP ACT.26: 4 residues within 4Å: Chain A: D.65, G.203, L.204, A.205 Ligand excluded by PLIP ACT.27: 6 residues within 4Å: Chain A: T.37, T.228, V.231, S.247 Ligands: ACT.5, ACT.20 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brown, M.E. et al., Identification and characterization of a multifunctional dye peroxidase from a lignin-reactive bacterium. Acs Chem.Biol. (2012)

Release Date

2012-10-24

Peptides

DyP2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DyP2

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