SMTL ID : 9dl7.3 (2 other biounits)

Structure of proline utilization A complexed with 1-(4-fluorophenyl)thiourea

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

monomer

Ligands

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

FAD.1: 29 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 28 PLIP interactions: 28 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:G.373, A:G.373, A:G.373, A:A.374, A:T.395, A:H.425, A:N.426, A:N.426, A:E.494, A:S.499, A:F.501 Water bridges: A:K.372, A:K.372, 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

1 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)

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

PEG.3: 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:T.548, A:R.689 PEG.4: 4 residues within 4Å: Chain A: D.1131, A.1133, R.1174, A.1177 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.1131, A:R.1174, A:R.1174 PEG.7: 1 residues within 4Å: Chain A: K.899 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.899 PEG.9: 5 residues within 4Å: Chain A: L.553, E.559, T.560, S.563, L.564 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.559, A:S.563

1 x 8P4: 1-(4-fluorophenyl)thiourea(Non-covalent)

8P4.5: 7 residues within 4Å: Chain A: I.705, K.732, G.765, G.768, A.769, V.788, I.792 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.705, A:V.788 Hydrogen bonds: A:G.768

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

FMT.6: 5 residues within 4Å: Chain A: S.1045, V.1046, G.1081, L.1082, D.1083 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.1045, A:V.1046, A:D.1083 FMT.8: 5 residues within 4Å: Chain A: D.386, L.553, D.554, L.555, L.668 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.554, A:L.555 Water bridges: A:L.553, A:L.553 FMT.10: 2 residues within 4Å: Chain A: S.1152, W.1153 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.1153 Water bridges: A:V.1151 FMT.11: 4 residues within 4Å: Chain A: T.584, G.585, P.586, R.617 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.584, A:R.617, A:R.617 FMT.12: 2 residues within 4Å: Chain A: S.611, E.612 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.612, A:E.612

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

SO4.13: 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 SO4.14: 8 residues within 4Å: Chain A: F.710, R.845, S.847, I.1003, G.1004, A.1005, F.1012 Ligands: SO4.18 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.847, A:S.847, A:G.1004, A:A.1005 Salt bridges: A:R.845 SO4.15: 2 residues within 4Å: Chain A: A.650, R.651 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.651 SO4.16: 6 residues within 4Å: Chain A: Q.384, R.535, I.536, A.537, G.1088, V.1090 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.384, A:A.537, A:A.537 Water bridges: A:G.1088 SO4.17: 7 residues within 4Å: Chain A: L.385, D.386, L.668, I.671, A.672, R.675 Ligands: SO4.20 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.385, A:L.668 Salt bridges: A:R.675 SO4.18: 5 residues within 4Å: Chain A: E.676, F.710, I.714, F.1012 Ligands: SO4.14 No protein-ligand interaction detected (PLIP) SO4.19: 6 residues within 4Å: Chain A: A.1100, G.1102, G.1125, N.1126, S.1127, R.1150 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.1125, A:S.1127 SO4.20: 5 residues within 4Å: Chain A: A.672, R.675, E.676, D.679 Ligands: SO4.17 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.679 Water bridges: A:R.675, A:R.675, A:D.679, A:D.679 Salt bridges: A:R.675 SO4.21: 5 residues within 4Å: Chain A: W.629, E.636, C.640, R.643, G.752 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.643 Water bridges: A:R.643, A:G.752 SO4.22: 8 residues within 4Å: Chain A: A.803, G.804, R.805, I.1175, A.1194, A.1195, S.1196, E.1199 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.1196, A:S.1196 Salt bridges: A:R.805

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