SMTL ID : 9dl6.3 (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: 31 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, S.499, S.500, F.501, I.1234, G.1235 33 PLIP interactions: 33 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:T.395, A:D.401, A:H.425, A:N.426, A:N.426, A:E.494, A:E.494, A:E.494, A:S.499, A:F.501, A:G.1235 Water bridges: A:A.423, A:E.494, A:E.494, A:V.502 Salt bridges: A:K.372, A:K.372, A:K.397 pi-Stacking: A:W.376, A:W.376, A:W.376

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

PGE.2: 6 residues within 4Å: Chain A: H.1047, L.1080, G.1081, L.1082, L.1098, H.1099 No protein-ligand interaction detected (PLIP) PGE.7: 5 residues within 4Å: Chain A: D.1156, W.1157, R.1174, A.1177, A.1181 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:W.1157, A:R.1174, A:A.1177 Water bridges: A:A.1158, A:R.1174, A:A.1181

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

PEG.3: 5 residues within 4Å: Chain A: G.544, D.545, 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 PEG.5: 4 residues within 4Å: Chain A: R.805, S.1196, S.1197, G.1198 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.805, A:R.805, A:S.1196, A:G.1198 Water bridges: A:S.1197, A:S.1197 PEG.8: 4 residues within 4Å: Chain A: R.282, H.871, E.872, L.873 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.282, A:L.873, A:H.874

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

PG4.4: 3 residues within 4Å: Chain A: N.896, K.899, R.941 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.899 Water bridges: A:R.941

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

FMT.6: 6 residues within 4Å: Chain A: G.1021, P.1022, R.1101, V.1213, E.1214, E.1215 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.1101, A:E.1215 Water bridges: A:G.1014, A:E.1214 FMT.9: 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:N.557, A:T.560

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

01.10: 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: ID7.11 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.710, A:F.710, A:I.714, A:F.1012, 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)

ID7.11: 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: 01.10 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

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

SO4.12: 3 residues within 4Å: Chain A: R.690, P.1041, Q.1042 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.1042 Water bridges: A:R.690, A:R.690, A:Q.1042 Salt bridges: A:R.690 SO4.13: 4 residues within 4Å: Chain A: R.71, S.511, I.512, D.513 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.512, A:D.513 Water bridges: A:R.78 Salt bridges: A:R.71

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

NAD.14: 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.15 17 PLIP interactions: 17 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:L.791, A:T.813, A:E.942

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

MG.15: 1 residues within 4Å: Ligands: NAD.14 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
B

Bifunctional protein PutA

Related Entries With Identical Sequence