SMTL ID : 9dl6.2 (2 other biounits)

Structure of proline utilization A complexed with piperidine-3-carboxylic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

monomer

Ligands

1 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, A.423, T.424, H.425, N.426, Q.449, C.450, L.451, Y.475, E.494, N.495, S.499, S.500, F.501, I.1234, G.1235 32 PLIP interactions: 32 interactions with chain A Hydrophobic interactions: A:A.423, A:Q.449, A:L.451, A:Y.475, 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:T.395, A:K.397, A:T.400, A:T.424, A:H.425, A:N.426, A:N.426, A:E.494, A:S.499, A:F.501 Water bridges: A:E.494, A:N.495, A:V.502 Salt bridges: A:K.372, A:K.372, A:K.397 pi-Stacking: A:W.376, A:W.376

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

PEG.2: 5 residues within 4Å: Chain A: Y.239, P.289, R.290, A.293 Ligands: FMT.7 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.290, A:R.290 PEG.4: 6 residues within 4Å: Chain A: A.1100, G.1102, G.1125, S.1127, L.1149, R.1150 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.1150 PEG.5: 4 residues within 4Å: Chain A: Y.434, H.435, G.438, K.439 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.438 Water bridges: A:Y.434, A:R.470 PEG.9: 6 residues within 4Å: Chain A: G.544, D.545, A.546, R.547, T.548, R.689 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.544 Water bridges: A:R.689, A:R.689

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

PGE.3: 8 residues within 4Å: Chain A: I.984, T.988, L.996, L.1095, T.1097, H.1099, A.1218, I.1220 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.988 PGE.10: 6 residues within 4Å: Chain A: L.1080, G.1081, L.1082, T.1097, L.1098, H.1099 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.1083

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

FMT.6: 5 residues within 4Å: Chain A: G.1021, P.1022, R.1101, E.1214, E.1215 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.1101, A:E.1215, A:E.1215, A:E.1215 Water bridges: A:R.1101 FMT.7: 3 residues within 4Å: Chain A: E.236, Y.239 Ligands: PEG.2 No protein-ligand interaction detected (PLIP) FMT.8: 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:R.42, A:A.389 Water bridges: A:D.554, A:D.554, A:T.560 FMT.20: 1 residues within 4Å: Chain A: T.864 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.864

1 x 01: (3S)-piperidine-3-carboxylic acid

01.11: 11 residues within 4Å: Chain A: E.676, F.710, I.714, R.845, C.846, S.847, I.1003, G.1004, A.1005, F.1012 Ligands: ID7.12 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.710, A:F.710, A:I.714, A:F.1012 Hydrogen bonds: A:S.847, A:G.1004, A:A.1005 Salt bridges: A:R.845

1 x ID7: (3R)-piperidine-3-carboxylic acid(Non-covalent)

ID7.12: 11 residues within 4Å: Chain A: E.676, F.710, I.714, R.845, C.846, S.847, I.1003, G.1004, A.1005, F.1012 Ligands: 01.11 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.710, A:F.710, A:I.714, A:F.1012 Hydrogen bonds: A:S.847, A:G.1004, A:A.1005 Water bridges: A:E.676 Salt bridges: A:R.845

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

SO4.13: 3 residues within 4Å: Chain A: R.690, P.1041, Q.1042 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.1042 Water bridges: A:R.690 Salt bridges: A:R.690 SO4.14: 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:D.857, A:R.955 Water bridges: A:D.956 Salt bridges: A:R.954 SO4.15: 4 residues within 4Å: Chain A: S.1196, G.1198, E.1199, R.1202 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.1196, A:G.1198, A:E.1199 Salt bridges: A:R.1202 SO4.16: 4 residues within 4Å: Chain A: K.1062, A.1138, K.1141, N.1142 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.1141 Salt bridges: A:K.1062 SO4.17: 4 residues within 4Å: Chain A: T.158, S.159, R.1093, A.1229 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.159, A:S.159 Water bridges: A:A.1229, A:A.1229 Salt bridges: A:R.1093

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

NAD.18: 31 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, I.792, E.812, T.813, G.814, C.846, E.942, F.944, L.972, F.1012, S.1018 Ligands: MG.19 18 PLIP interactions: 18 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.736, A:T.786, A:T.813, A:E.942, A:E.942, A:E.942

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

MG.19: 1 residues within 4Å: Ligands: NAD.18 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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Bifunctional protein PutA

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