SMTL ID : 4nmf.1

Crystal structure of proline utilization A (PutA) from Geobacter sulfurreducens PCA inactivated by N-propargylglycine and complexed with menadione bisulfite

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x P5F: N-propargylglycine-modified flavin adenine dinucleotide(Covalent)

P5F.1: 32 residues within 4Å: Chain A: K.204, 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, V.385, L.386, Y.407, E.426, E.431, S.432, F.433 Ligands: 2L3.2 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:K.204, A:A.357, A:Q.384, A:L.386, A:L.386, A:Y.407, A:Y.407, 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:H.359, A:N.360, A:N.360, A:E.426, A:F.433 Water bridges: A:K.331, A:A.357 Salt bridges: A:K.307, A:K.307, A:K.331 pi-Stacking: A:W.311, A:W.311 P5F.8: 33 residues within 4Å: Chain B: K.204, 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, V.385, L.386, Y.407, E.426, E.431, S.432, F.433 Ligands: 2L3.9, 2LB.10 33 PLIP interactions: 33 interactions with chain B Hydrophobic interactions: B:K.204, B:D.245, B:A.357, B:Q.384, B:L.386, B:L.386, B:Y.407, 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:H.359, B:N.360, B:N.360, B:E.426, B:E.431, B:F.433 Water bridges: B:Y.310, B:K.331, B:E.426 Salt bridges: B:K.307, B:K.307, B:K.331 pi-Stacking: B:W.311, B:W.311

2 x 2L3: (2R)-2-methyl-1,4-dioxo-1,2,3,4-tetrahydronaphthalene-2-sulfonic acid(Non-covalent)

2L3.2: 9 residues within 4Å: Chain A: D.146, K.204, A.309, Y.310, Y.407, Y.419, R.422, R.423 Ligands: P5F.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.309, A:Y.310, A:Y.407, A:Y.419 Water bridges: A:R.422 Salt bridges: A:R.422, A:R.423 pi-Cation interactions: A:K.204 2L3.9: 10 residues within 4Å: Chain B: D.146, K.204, A.309, Y.310, Y.407, Y.419, R.422, R.423 Ligands: P5F.8, 2LB.10 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:A.309, B:Y.310, B:Y.407, B:Y.419, B:Y.419 Hydrogen bonds: B:K.204 Salt bridges: B:R.422, B:R.423

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 6 residues within 4Å: Chain A: W.328, E.333, A.336, A.337, R.340, R.459 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.328, A:A.337, A:R.340, A:R.340 EDO.4: 5 residues within 4Å: Chain A: Y.313, K.317, Q.320 Chain B: N.988, M.990 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.317, A:Q.320, B:N.988 Water bridges: A:Q.320 EDO.5: 4 residues within 4Å: Chain A: Y.249, W.323, D.486, T.488 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.486, A:T.488 EDO.6: 5 residues within 4Å: Chain A: F.479, Y.617, R.620, E.621, E.954 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.621, A:E.621 Water bridges: A:R.624, A:E.954 EDO.7: 5 residues within 4Å: Chain A: D.771, L.803, D.804, A.805, K.902 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.805 Water bridges: A:D.771 EDO.11: 5 residues within 4Å: Chain B: F.479, Y.617, R.620, E.621, E.954 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.621, B:E.954 Water bridges: B:R.624 EDO.12: 6 residues within 4Å: Chain B: Y.249, W.323, E.324, P.326, D.486, T.488 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.486 Water bridges: B:Y.249, B:A.318, B:T.488 EDO.13: 5 residues within 4Å: Chain A: Q.320, R.946 Chain B: E.637, T.986, N.988 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.946

1 x 2LB: (2S)-2-methyl-1,4-dioxo-1,2,3,4-tetrahydronaphthalene-2-sulfonic acid(Non-covalent)

2LB.10: 10 residues within 4Å: Chain B: D.146, K.204, A.309, Y.310, L.386, Y.419, R.422, R.423 Ligands: P5F.8, 2L3.9 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.309, B:L.386, B:Y.419 Hydrogen bonds: B:R.422 Water bridges: B:Y.310 Salt bridges: B:R.422

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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