SMTL ID : 9dl7.1 (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

homo-dimer

Ligands

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

FAD.1: 28 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, S.499, S.500, F.501 26 PLIP interactions: 26 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: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 Salt bridges: A:K.372, A:K.372, A:K.397 pi-Stacking: A:Y.475 FAD.31: 29 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 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:G.373, B:G.373, B:G.373, B:A.374, B:T.395, B:H.425, B:N.426, B:N.426, B:E.494, B:S.499, B:F.501 Water bridges: B:K.372, B:K.372, B:E.494, B:E.494, B:V.502 Salt bridges: B:K.372, B:K.372, B:K.397 pi-Stacking: B:W.376, B:W.376

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

PEG.2: 3 residues within 4Å: Chain A: Y.239, P.289, R.290 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.290, A:R.290 PEG.4: 7 residues within 4Å: Chain A: D.1131, A.1133, W.1157, R.1174, A.1177, A.1181 Ligands: SO4.19 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.1131, A:R.1174, A:R.1174 PEG.7: 6 residues within 4Å: Chain A: K.575, W.576, T.577, R.651, E.743, R.746 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.577, A:T.577, A:R.651, A:R.746, A:R.746 Water bridges: A:E.743 PEG.12: 4 residues within 4Å: Chain A: R.274, T.836, D.840, L.873 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.840 Water bridges: A:T.836 PEG.33: 6 residues within 4Å: Chain B: G.544, D.545, A.546, R.547, T.548, R.689 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.544 Water bridges: B:T.548, B:R.689 PEG.34: 4 residues within 4Å: Chain B: D.1131, A.1133, R.1174, A.1177 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.1131, B:R.1174, B:R.1174 PEG.37: 1 residues within 4Å: Chain B: K.899 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.899 PEG.39: 5 residues within 4Å: Chain B: L.553, E.559, T.560, S.563, L.564 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.559, B:S.563

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

PGE.3: 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.32: 6 residues within 4Å: Chain B: H.1047, L.1080, G.1081, L.1082, L.1098, H.1099 No protein-ligand interaction detected (PLIP)

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

8P4.5: 8 residues within 4Å: Chain A: K.732, G.765, G.768, A.769, V.772, V.788, I.792, Q.795 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.772, A:V.788, A:I.792 Water bridges: A:K.732, A:K.732 8P4.35: 7 residues within 4Å: Chain B: I.705, K.732, G.765, G.768, A.769, V.788, I.792 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.705, B:V.788 Hydrogen bonds: B:G.768

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

FMT.6: 6 residues within 4Å: Chain A: D.386, L.553, D.554, L.555, L.668 Ligands: SO4.22 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.555 Water bridges: A:L.553 FMT.8: 4 residues within 4Å: Chain A: T.158, S.159, R.1093, T.1222 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.159, A:S.159, A:R.1093, A:R.1093 Water bridges: A:T.160 FMT.9: 3 residues within 4Å: Chain A: H.696, A.1037 Chain B: S.175 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.696, B:S.175 Water bridges: A:V.1039 FMT.10: 4 residues within 4Å: Chain A: G.544, D.545, R.547, T.548 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.548 Water bridges: A:T.548 FMT.11: 2 residues within 4Å: Chain A: S.611, E.612 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.612 Water bridges: A:E.613 FMT.13: 5 residues within 4Å: Chain A: S.1045, V.1046, G.1081, L.1082, D.1083 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.1046, A:G.1081, A:D.1083 Water bridges: B:N.162 FMT.14: 5 residues within 4Å: Chain A: S.175 Chain B: H.696, T.1036, A.1037, P.1038 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.175 Water bridges: B:V.1039 FMT.36: 5 residues within 4Å: Chain B: S.1045, V.1046, G.1081, L.1082, D.1083 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.1045, B:V.1046, B:D.1083 Water bridges: A:N.162, A:N.162, A:N.162 FMT.38: 5 residues within 4Å: Chain B: D.386, L.553, D.554, L.555, L.668 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.554, B:L.555 Water bridges: B:L.553, B:L.553 FMT.40: 2 residues within 4Å: Chain B: S.1152, W.1153 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.1153 Water bridges: B:V.1151 FMT.41: 4 residues within 4Å: Chain B: T.584, G.585, P.586, R.617 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.584, B:R.617, B:R.617 FMT.42: 2 residues within 4Å: Chain B: S.611, E.612 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.612, B:E.612

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

SO4.15: 8 residues within 4Å: Chain A: R.690, P.1041, Q.1042 Chain B: S.96, Q.98, E.99, A.169, R.172 Ligand excluded by PLIP SO4.16: 7 residues within 4Å: Chain A: F.710, R.845, S.847, I.1003, G.1004, A.1005, F.1012 Ligand excluded by PLIP SO4.17: 2 residues within 4Å: Chain A: S.332, G.333 Ligand excluded by PLIP SO4.18: 2 residues within 4Å: Chain A: K.1062, A.1138 Ligand excluded by PLIP SO4.19: 4 residues within 4Å: Chain A: K.1155, D.1156, W.1157 Ligands: PEG.4 Ligand excluded by PLIP SO4.20: 5 residues within 4Å: Chain A: A.67, S.68, R.71, D.513, I.516 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain A: R.360, R.361, G.363 Ligand excluded by PLIP SO4.22: 7 residues within 4Å: Chain A: D.386, L.668, I.671, A.672, R.675 Ligands: FMT.6, SO4.23 Ligand excluded by PLIP SO4.23: 4 residues within 4Å: Chain A: A.672, R.675, D.679 Ligands: SO4.22 Ligand excluded by PLIP SO4.24: 6 residues within 4Å: Chain A: Q.384, R.535, I.536, A.537, G.1088, V.1090 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain A: S.1196, G.1198, R.1202 Ligand excluded by PLIP SO4.26: 4 residues within 4Å: Chain A: R.282, H.871, E.872, L.873 Ligand excluded by PLIP SO4.27: 5 residues within 4Å: Chain A: P.273, R.274, Y.275, S.276, R.314 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain A: R.71, S.511, I.512, D.513 Ligand excluded by PLIP SO4.29: 7 residues within 4Å: Chain A: A.803, G.804, R.805, A.1194, A.1195, S.1196, E.1199 Ligand excluded by PLIP SO4.30: 6 residues within 4Å: Chain A: Q.855, E.856, D.857, Y.953, R.954, R.955 Ligand excluded by PLIP SO4.43: 8 residues within 4Å: Chain A: S.96, Q.98, E.99, A.169, R.172 Chain B: R.690, P.1041, Q.1042 Ligand excluded by PLIP SO4.44: 8 residues within 4Å: Chain B: F.710, R.845, S.847, I.1003, G.1004, A.1005, F.1012 Ligands: SO4.48 Ligand excluded by PLIP SO4.45: 2 residues within 4Å: Chain B: A.650, R.651 Ligand excluded by PLIP SO4.46: 6 residues within 4Å: Chain B: Q.384, R.535, I.536, A.537, G.1088, V.1090 Ligand excluded by PLIP SO4.47: 7 residues within 4Å: Chain B: L.385, D.386, L.668, I.671, A.672, R.675 Ligands: SO4.50 Ligand excluded by PLIP SO4.48: 5 residues within 4Å: Chain B: E.676, F.710, I.714, F.1012 Ligands: SO4.44 Ligand excluded by PLIP SO4.49: 6 residues within 4Å: Chain B: A.1100, G.1102, G.1125, N.1126, S.1127, R.1150 Ligand excluded by PLIP SO4.50: 5 residues within 4Å: Chain B: A.672, R.675, E.676, D.679 Ligands: SO4.47 Ligand excluded by PLIP SO4.51: 5 residues within 4Å: Chain B: W.629, E.636, C.640, R.643, G.752 Ligand excluded by PLIP SO4.52: 8 residues within 4Å: Chain B: A.803, G.804, R.805, I.1175, A.1194, A.1195, S.1196, E.1199 Ligand excluded by 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

Related Entries With Identical Sequence