SMTL ID : 4v4d.2 (11 other biounits)

Crystal Structure of Pyrogallol-Phloroglucinol Transhydroxylase from Pelobacter acidigallici complexed with pyrogallol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-mer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: W.339, A.340, K.342, Q.377 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:W.339, A:A.340, A:K.342 CA.6: 4 residues within 4Å: Chain A: R.257 Chain B: I.61, N.62, R.193 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:I.61, A:R.257, H2O.27, H2O.30, H2O.32

2 x MGD: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE(Non-covalent)

MGD.2: 35 residues within 4Å: Chain A: S.142, S.143, H.144, H.145, M.146, D.174, S.175, R.359, R.449, Y.496, G.497, G.498, P.499, T.503, Q.525, S.526, I.527, W.528, A.542, D.589, S.736, P.737, H.738, H.744, T.745, M.746, E.818, N.840, T.843, M.855, N.857, N.858 Ligands: MGD.3, 4MO.4, PYG.5 28 PLIP interactions: 28 interactions with chain A Hydrogen bonds: A:S.142, A:S.143, A:H.144, A:M.146, A:R.359, A:G.498, A:T.503, A:Q.525, A:H.738, A:T.745, A:T.745, A:M.746, A:N.840, A:N.840, A:N.857, A:N.858, A:N.858 Water bridges: A:E.530, A:E.530, A:R.548, A:D.589, A:T.745, A:T.745 Salt bridges: A:D.589, A:H.744, A:E.818 pi-Stacking: A:H.145 pi-Cation interactions: A:Y.496 MGD.3: 35 residues within 4Å: Chain A: Y.62, H.144, S.175, W.215, S.216, D.218, T.221, N.222, G.224, I.225, I.248, D.249, P.250, H.251, N.253, D.271, G.350, W.354, G.355, G.356, A.357, R.359, H.362, L.735, P.737, H.738, P.739, R.740, S.742, M.743, H.744, N.858 Ligands: MGD.2, 4MO.4, PYG.5 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:S.216, A:D.218, A:D.218, A:T.221, A:N.222, A:N.222, A:I.248, A:N.253, A:G.350, A:G.355, A:G.356, A:H.738, A:H.738, A:S.742, A:H.744 Water bridges: A:Y.62, A:G.224, A:Y.226, A:H.251, A:G.269, A:Y.817 Salt bridges: A:D.249, A:D.271, A:R.359, A:R.359, A:H.738, A:H.738

1 x 4MO: MOLYBDENUM(IV) ION(Covalent)

4MO.4: 7 residues within 4Å: Chain A: H.144, D.174, S.175, H.738 Ligands: MGD.2, MGD.3, PYG.5 No protein-ligand interaction detected (PLIP)

1 x PYG: BENZENE-1,2,3-TRIOL(Non-covalent)

PYG.5: 14 residues within 4Å: Chain A: S.143, H.144, R.153, D.174, S.175, W.176, I.225, W.354, Y.404, F.468, C.557 Ligands: MGD.2, MGD.3, 4MO.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.176, A:I.225, A:W.354 Hydrogen bonds: A:R.153, A:D.174 Water bridges: A:Y.404 pi-Stacking: A:H.144

3 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.7: 13 residues within 4Å: Chain B: C.13, Q.14, D.15, C.16, N.17, N.18, C.19, I.48, P.65, C.149, S.151, V.153, Y.154 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.13, B:C.16, B:C.19, B:C.149 SF4.8: 11 residues within 4Å: Chain B: C.23, H.27, M.46, P.67, C.126, T.127, M.128, C.129, P.143, R.144, C.145 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.23, B:C.126, B:C.129, B:C.145 SF4.9: 12 residues within 4Å: Chain B: C.68, M.69, H.70, C.71, A.74, P.75, C.76, V.92, C.109, P.110, V.113, K.125 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.68, B:C.71, B:C.76, B:C.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Messerschmidt, A. et al., Crystal structure of pyrogallol-phloroglucinol transhydroxylase, an Mo enzyme capable of intermolecular hydroxyl transfer between phenols. PROC.NATL.ACAD.SCI.USA (2004)

Release Date

2014-07-09

Peptides

Pyrogallol hydroxytransferase large subunit: A
Pyrogallol hydroxytransferase small subunit: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Pyrogallol hydroxytransferase large subunit

Pyrogallol hydroxytransferase small subunit

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