SMTL ID : 9e0d.1 (2 other biounits)

Structure of proline utilization A complexed with piperonyl alcohol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.33 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 32 residues within 4Å: Chain A: D.308, A.309, V.340, Q.342, Y.344, R.369, V.371, K.372, G.373, A.374, Y.375, W.376, F.394, T.395, R.396, K.397, T.400, D.401, A.423, T.424, H.425, N.426, Q.449, C.450, L.451, Y.475, S.499, S.500, F.501, I.1234, G.1235 Ligands: 01.5 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:A.423, A:Q.449, A:Y.475 Hydrogen bonds: A:A.309, A:A.309, A:Q.342, A:R.369, A:K.372, A:G.373, A:G.373, A:G.373, A:A.374, A:K.397, A:T.400, A:D.401, A:T.424, A:H.425, A:H.425, A:N.426, A:S.499, A:F.501, A:I.1234 Water bridges: A:A.423, A:V.502 Salt bridges: A:K.372, A:K.372, A:K.397 pi-Stacking: A:W.376, A:W.376 FAD.13: 32 residues within 4Å: Chain B: D.308, A.309, V.340, Q.342, Y.344, R.369, V.371, K.372, G.373, A.374, Y.375, W.376, F.394, T.395, R.396, K.397, T.400, A.423, T.424, H.425, N.426, Q.449, C.450, L.451, Y.475, E.494, S.499, S.500, F.501, I.1234, G.1235 Ligands: 01.19 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:A.423, B:Q.449, B:Y.475 Hydrogen bonds: B:A.309, B:A.309, B:Q.342, B:R.369, B:K.372, B:G.373, B:G.373, B:G.373, B:A.374, B:T.395, B:D.401, B:T.424, B:H.425, B:N.426, B:N.426, B:S.499, B:F.501, B:G.1235 Water bridges: B:V.502 Salt bridges: B:K.372, B:K.372, B:K.397 pi-Stacking: B:W.376, B:W.376, B:W.376

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2: 6 residues within 4Å: Chain A: H.1047, L.1080, G.1081, D.1083, L.1098, H.1099 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.1083 PGE.15: 6 residues within 4Å: Chain B: H.1047, L.1080, G.1081, D.1083, L.1098, H.1099 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.1083

4 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 2 residues within 4Å: Chain A: P.19, D.602 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.602 Water bridges: A:P.17, A:V.603, A:R.661 FMT.4: 4 residues within 4Å: Chain A: R.42, L.388, A.389, D.554 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.389 Water bridges: A:R.42, A:D.554, A:D.554, A:T.560 FMT.14: 6 residues within 4Å: Chain B: G.1021, P.1022, R.1101, V.1213, E.1214, E.1215 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.1101, B:E.1215, B:E.1215 Water bridges: B:E.1214 FMT.18: 4 residues within 4Å: Chain B: R.42, L.388, A.389, D.554 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.389 Water bridges: B:D.554, B:N.557, B:T.560

2 x 01: (2H-1,3-benzodioxol-5-yl)methanol

01.5: 8 residues within 4Å: Chain A: K.267, D.308, A.309, A.374, Y.375, Y.475, R.490 Ligands: FAD.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.475, A:Y.475 Hydrogen bonds: A:K.267, A:Y.375, A:R.490 01.19: 9 residues within 4Å: Chain B: K.267, D.308, A.309, A.374, Y.375, L.451, Y.475, R.490 Ligands: FAD.13 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.475, B:Y.475 Hydrogen bonds: B:K.267, B:D.308

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.6: 32 residues within 4Å: Chain A: I.705, S.706, P.707, W.708, N.709, F.710, I.714, K.732, P.733, A.734, E.735, D.764, G.765, G.768, A.769, F.782, T.783, G.784, S.785, V.788, L.791, I.792, E.812, T.813, G.814, C.846, E.942, F.944, L.972, F.1012, S.1018 Ligands: MG.12 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:P.707, A:F.710, A:I.714, A:T.783 Hydrogen bonds: A:S.706, A:S.706, A:W.708, A:K.732, A:E.735, A:S.785, A:T.813, A:E.942 Water bridges: A:E.735, A:E.736, A:E.736, A:E.736, A:E.736, A:S.785, A:S.785, A:T.786, A:Q.795, A:T.813, A:E.942, A:E.942, A:E.942, A:E.942 NAD.20: 32 residues within 4Å: Chain B: I.705, S.706, P.707, W.708, N.709, F.710, I.714, K.732, P.733, A.734, E.735, D.764, G.765, G.768, A.769, F.782, T.783, G.784, S.785, V.788, L.791, I.792, E.812, T.813, G.814, C.846, E.942, F.944, L.972, F.1012, S.1018 Ligands: MG.22 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:P.707, B:F.710, B:I.714, B:T.783 Hydrogen bonds: B:S.706, B:S.706, B:W.708, B:K.732, B:E.735, B:S.785, B:T.813, B:E.942 Water bridges: B:E.736, B:E.736, B:S.785, B:S.785, B:T.786, B:Q.795, B:T.813, B:E.942

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 8 residues within 4Å: Chain A: R.690, P.1041, Q.1042 Chain B: S.96, Q.98, E.99, A.169, R.172 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:S.96, B:E.99, A:Q.1042 Water bridges: B:S.96, B:S.97, B:R.172, B:R.172, A:R.690, A:R.690 Salt bridges: B:R.172, A:R.690 SO4.8: 3 residues within 4Å: Chain A: S.1196, G.1198, R.1202 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.1196, A:G.1198, A:E.1199 Water bridges: A:R.1202, A:R.1202 Salt bridges: A:R.1202 SO4.9: 2 residues within 4Å: Chain A: K.1062, A.1138 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.1062 SO4.10: 6 residues within 4Å: Chain A: S.139, Q.855, E.856, D.857, R.954, R.955 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.855, A:E.856, A:D.857, A:R.955 Water bridges: A:D.956 SO4.11: 4 residues within 4Å: Chain A: R.71, S.511, I.512, D.513 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.512, A:D.513 Salt bridges: A:R.71 SO4.21: 8 residues within 4Å: Chain A: S.96, Q.98, E.99, A.169, R.172 Chain B: R.690, P.1041, Q.1042 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:S.96, A:S.96, B:Q.1042 Water bridges: A:S.97, A:S.165, A:S.165, A:R.172, B:R.690, B:Q.1042 Salt bridges: A:R.172, B:R.690

2 x MG: MAGNESIUM ION(Non-functional Binders)

MG.12: 1 residues within 4Å: Ligands: NAD.6 No protein-ligand interaction detected (PLIP) MG.22: 1 residues within 4Å: Ligands: NAD.20 No protein-ligand interaction detected (PLIP)

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.16: 3 residues within 4Å: Chain B: N.896, K.899, R.941 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.899

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.17: 5 residues within 4Å: Chain B: R.805, S.1196, S.1197, G.1198, R.1202 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:R.805, B:R.805, B:S.1196, B:G.1198, B:R.1202, B:R.1202 Water bridges: B:A.803, B:S.1197, B:S.1197 PEG.23: 2 residues within 4Å: Chain B: A.583, T.584 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meeks, K.R. et al., Crystallographic Fragment Screening of a Bifunctional Proline Catabolic Enzyme Reveals New Inhibitor Templates for Proline Dehydrogenase and L-Glutamate-gamma-semialdehyde Dehydrogenase. Molecules (2024)

Release Date

2024-11-27

Peptides

Bifunctional protein PutA: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Bifunctional protein PutA

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