SMTL ID : 4nmc.1

Crystal structure of oxidized proline utilization A (PutA) from Geobacter sulfurreducens PCA complexed with Zwittergent 3-12

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 25 residues within 4Å: Chain A: D.245, M.246, V.275, Q.277, Y.279, R.304, V.306, K.307, G.308, A.309, Y.310, W.311, W.328, T.329, I.330, K.331, S.334, D.335, A.357, S.358, H.359, N.360, Q.384, L.386, Y.407 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:A.357, A:Q.384, A:L.386, A:Y.407 Hydrogen bonds: A:M.246, A:M.246, A:Q.277, A:R.304, A:K.307, A:G.308, A:G.308, A:G.308, A:A.309, A:T.329, A:S.334, A:D.335, A:H.359, A:N.360, A:N.360 Salt bridges: A:K.307, A:K.307, A:K.331 pi-Stacking: A:W.311, A:W.311, A:Y.407 FAD.4: 31 residues within 4Å: Chain B: D.245, M.246, V.275, Q.277, Y.279, R.304, V.306, K.307, G.308, A.309, Y.310, W.311, W.328, T.329, I.330, K.331, S.334, A.357, S.358, H.359, N.360, Q.384, V.385, L.386, Y.407, R.423, E.426, E.431, S.432, F.433 Ligands: 2OP.9 34 PLIP interactions: 34 interactions with chain B Hydrophobic interactions: B:A.357, B:Q.384, B:L.386, B:L.386, B:Y.407 Hydrogen bonds: B:M.246, B:M.246, B:Q.277, B:R.304, B:K.307, B:G.308, B:G.308, B:G.308, B:A.309, B:T.329, B:S.334, B:D.335, B:S.358, B:H.359, B:N.360, B:N.360, B:E.426, B:F.433 Water bridges: B:K.204, B:Y.310, B:K.331, B:E.426, B:L.434, B:L.434 Salt bridges: B:K.307, B:K.307, B:K.331 pi-Stacking: B:W.311, B:W.311

3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.2: 3 residues within 4Å: Chain A: H.640, F.642 Chain B: R.934 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:E.644, A:R.983, B:R.934 PG4.5: 10 residues within 4Å: Chain A: V.754, K.755, K.756, I.757, V.966 Chain B: V.754, K.755, K.756, I.757, V.966 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Water bridges: B:V.754, A:I.757, A:I.757, A:V.966, A:V.966 PG4.6: 3 residues within 4Å: Chain A: R.934 Chain B: H.640, F.642 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.934

2 x K: POTASSIUM ION(Non-covalent)

K.3: 4 residues within 4Å: Chain A: T.528, V.529, E.596, I.683 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:V.529, A:E.596, A:I.683, H2O.1, H2O.14 K.7: 4 residues within 4Å: Chain B: T.528, V.529, E.596, I.683 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:V.529, B:E.596, B:I.683, H2O.21, H2O.29

1 x C15: N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE(Non-covalent)

C15.8: 3 residues within 4Å: Chain B: W.35, F.77, L.109 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.35, B:F.77, B:L.109

1 x 2OP: (2S)-2-HYDROXYPROPANOIC ACID(Non-covalent)

2OP.9: 9 residues within 4Å: Chain B: K.204, D.245, A.309, L.386, Y.407, Y.419, R.422, R.423 Ligands: FAD.4 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.386 Hydrogen bonds: B:K.204, B:K.204 Water bridges: B:Y.310 Salt bridges: B:K.204, B:R.422, B:R.423

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, H. et al., Structures of the PutA peripheral membrane flavoenzyme reveal a dynamic substrate-channeling tunnel and the quinone-binding site. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-02-19

Peptides

Proline dehydrogenase and Delta-1-pyrroline-5-carboxylate dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Proline dehydrogenase and Delta-1-pyrroline-5-carboxylate dehydrogenase

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