SMTL ID : 6b9r.1 (1 other biounit)

Streptomyces albus HEPD with substrate 2-hydroxyethylphosphonate (2-HEP) and Fe(II) bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x FE: FE (III) ION(Non-covalent)

FE.1: 6 residues within 4Å: Chain A: N.146, H.149, Q.153, H.190 Chain B: K.29 Ligands: 2HE.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.149, A:H.190, H2O.5 FE.4: 4 residues within 4Å: Chain B: N.146, H.149, H.190 Ligands: 2HE.5 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.149, B:H.190, H2O.19, H2O.31

2 x 2HE: (2-hydroxyethyl)phosphonic acid(Non-covalent)

2HE.2: 12 residues within 4Å: Chain A: R.103, Y.109, Y.111, I.127, N.146, H.149, Q.153, H.190, F.192 Chain B: K.29, W.449 Ligands: FE.1 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:K.29, B:W.449, A:R.103, A:R.103, A:N.146, A:Q.153 Water bridges: B:K.29, B:K.29 2HE.5: 11 residues within 4Å: Chain A: K.29, W.449 Chain B: R.103, Y.109, Y.111, I.127, N.146, H.149, H.190, F.192 Ligands: FE.4 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.103, B:R.103, B:Y.111, B:N.146, A:W.449, A:W.449 Water bridges: B:N.146, A:K.29

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: D.81, R.87, M.116, R.118 Chain B: P.69 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.118, A:R.118 Water bridges: A:M.116 GOL.6: 8 residues within 4Å: Chain A: R.249 Chain B: Q.332, L.333, A.334, T.342, T.343, S.344, L.345 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.249, B:S.344, B:S.344 Water bridges: A:G.290, B:G.335 GOL.7: 5 residues within 4Å: Chain A: P.69 Chain B: D.81, R.87, M.116, R.118 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.118, B:R.118 Water bridges: B:M.116, B:M.116 GOL.8: 7 residues within 4Å: Chain B: V.91, S.94, E.95, R.112, W.126, Y.368, G.393 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.94, B:S.94, B:R.112, B:W.126 Water bridges: B:E.95 GOL.9: 6 residues within 4Å: Chain A: P.360, T.361, Y.362, R.428 Chain B: R.243, S.244 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:S.230, A:Y.362, A:R.428, A:R.428 Water bridges: B:R.243, B:S.244, A:P.360 GOL.10: 2 residues within 4Å: Chain B: H.172, C.173 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.172, B:C.173, B:C.173

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Born, D.A. et al., Structural basis for methylphosphonate biosynthesis. Science (2017)

Release Date

2017-12-20

Peptides

Hydroxyethylphosphonate dioxygenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Hydroxyethylphosphonate dioxygenase

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