SMTL ID : 9dl8.1 (2 other biounits)

Structure of proline utilization A soaked with 4-methoxybenzyl alcohol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

homo-dimer

Ligands

2 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, D.401, A.423, T.424, H.425, N.426, Q.449, C.450, L.451, Y.475, E.494, S.499, S.500, F.501 Ligands: 01.9 32 PLIP interactions: 32 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:N.426, A:E.494, A:S.499, A:F.501 Water bridges: A:R.491, 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 FAD.27: 30 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 Ligands: 01.34 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: B:A.423, B:Q.449, B:Y.475, 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:H.425, B:N.426, B:N.426, B:E.494, B:S.499, B:F.501 Water bridges: B:K.397, B:R.491, 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

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

PEG.2: 5 residues within 4Å: Chain A: E.236, Y.239, P.289, R.290, A.293 Ligand excluded by PLIP PEG.3: 5 residues within 4Å: Chain A: H.1047, L.1080, G.1081, L.1098, H.1099 Ligand excluded by PLIP PEG.4: 6 residues within 4Å: Chain A: L.385, D.386, A.672, R.675, D.679, V.1006 Ligand excluded by PLIP PEG.5: 6 residues within 4Å: Chain A: G.1102, R.1103, G.1125, S.1127, L.1149, R.1150 Ligand excluded by PLIP PEG.6: 6 residues within 4Å: Chain A: D.1131, A.1133, W.1157, R.1174, A.1177, A.1181 Ligand excluded by PLIP PEG.7: 5 residues within 4Å: Chain A: G.544, D.545, R.547, T.548, R.689 Ligand excluded by PLIP PEG.8: 5 residues within 4Å: Chain A: R.382, R.1000, N.1001, I.1003, G.1004 Ligand excluded by PLIP PEG.10: 6 residues within 4Å: Chain A: T.988, T.1097, H.1099, V.1216, A.1218, I.1220 Ligand excluded by PLIP PEG.12: 5 residues within 4Å: Chain A: M.574, K.575, V.603, V.604, S.606 Ligand excluded by PLIP PEG.15: 7 residues within 4Å: Chain A: A.1070, H.1116, I.1200, A.1201, R.1202, N.1203, P.1204 Ligand excluded by PLIP PEG.16: 5 residues within 4Å: Chain A: P.25, P.26, V.27, A.280, A.281 Ligand excluded by PLIP PEG.17: 8 residues within 4Å: Chain A: A.1070, A.1074, S.1077, H.1116, A.1120, P.1204, Y.1207, L.1209 Ligand excluded by PLIP PEG.20: 4 residues within 4Å: Chain A: A.639, D.642, R.643, E.646 Ligand excluded by PLIP PEG.28: 5 residues within 4Å: Chain B: D.1131, A.1133, W.1157, R.1174, A.1177 Ligand excluded by PLIP PEG.30: 4 residues within 4Å: Chain B: Y.239, R.240, P.289, R.290 Ligand excluded by PLIP PEG.31: 5 residues within 4Å: Chain B: G.544, D.545, R.547, T.548, R.689 Ligand excluded by PLIP PEG.32: 4 residues within 4Å: Chain B: S.1196, S.1197, G.1198, R.1202 Ligand excluded by PLIP PEG.33: 5 residues within 4Å: Chain B: G.1102, G.1125, S.1127, L.1149, R.1150 Ligand excluded by PLIP PEG.35: 5 residues within 4Å: Chain B: L.553, T.560, S.563, L.564, P.653 Ligand excluded by PLIP PEG.37: 5 residues within 4Å: Chain B: T.988, T.1097, H.1099, V.1216, I.1220 Ligand excluded by PLIP PEG.42: 4 residues within 4Å: Chain B: Y.434, H.435, G.438, K.439 Ligand excluded by PLIP PEG.44: 9 residues within 4Å: Chain B: A.1070, A.1074, H.1116, A.1119, A.1120, P.1204, D.1205, Y.1207, L.1209 Ligand excluded by PLIP

2 x 01: (4-methoxyphenyl)methanol

01.9: 8 residues within 4Å: Chain A: K.267, D.308, A.309, A.374, Y.375, Y.475, R.491 Ligands: FAD.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.374, A:Y.475 Hydrogen bonds: A:Y.375, A:Y.375 01.34: 9 residues within 4Å: Chain B: K.267, D.308, A.309, A.374, Y.375, L.451, Y.475, R.491 Ligands: FAD.27 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.374, B:Y.475 Hydrogen bonds: B:Y.375

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

PGE.11: 7 residues within 4Å: Chain A: D.534, R.535, A.537, E.541, L.542, F.543, G.544 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.541 Water bridges: A:D.545 PGE.29: 6 residues within 4Å: Chain B: H.1047, G.1081, L.1082, D.1083, L.1098, H.1099 No protein-ligand interaction detected (PLIP) PGE.40: 10 residues within 4Å: Chain B: L.385, D.386, L.388, G.552, L.553, I.671, A.672, R.675, D.679, V.1006 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:L.553, B:R.675, B:D.679 Water bridges: B:N.549, B:R.675, B:D.679

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

PG4.13: 7 residues within 4Å: Chain A: N.557, E.559, T.560, S.563, L.564, P.653 Ligands: FMT.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.563, A:S.563 Water bridges: A:N.557, A:A.567 PG4.18: 6 residues within 4Å: Chain A: S.332, G.333, W.334, N.335, G.363, R.364 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.332, A:G.333, A:W.334, A:R.364 PG4.36: 4 residues within 4Å: Chain B: R.790, A.1183, A.1184, L.1185 No protein-ligand interaction detected (PLIP) PG4.38: 2 residues within 4Å: Chain B: N.896, K.899 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.896, B:K.899

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

FMT.14: 5 residues within 4Å: Chain A: R.42, L.388, A.389, D.554 Ligands: PG4.13 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 FMT.19: 6 residues within 4Å: Chain A: A.803, G.804, I.1175, A.1195, S.1196, E.1199 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.804, A:S.1196 Water bridges: A:S.1196, A:E.1199 FMT.21: 5 residues within 4Å: Chain A: A.625, D.628, W.629, P.754, S.756 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.756 FMT.39: 6 residues within 4Å: Chain B: N.896, R.941, E.942, V.943, F.944 Ligands: NAD.45 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.942, B:F.944 FMT.41: 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 FMT.43: 3 residues within 4Å: Chain A: R.690 Chain B: S.94, L.95 No protein-ligand interaction detected (PLIP)

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

NAD.22: 28 residues within 4Å: Chain A: I.705, S.706, P.707, W.708, N.709, 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 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.714, A:T.783, A:E.812 Hydrogen bonds: A:S.706, A:W.708, A:K.732, A:E.735, A:S.785, A:E.812, A:E.942, A:S.1018 Water bridges: A:T.786 NAD.45: 26 residues within 4Å: Chain B: I.705, S.706, P.707, W.708, N.709, K.732, P.733, A.734, 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 Ligands: FMT.39, MG.48 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:P.707 Hydrogen bonds: B:S.706, B:N.709, B:K.732, B:G.784, B:S.785, B:E.812 Water bridges: B:E.735, B:E.735, B:E.735, B:E.736, B:S.785, B:N.896, B:F.944 pi-Stacking: B:F.944

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

SO4.23: 8 residues within 4Å: Chain A: R.690, P.1041, Q.1042 Chain B: S.96, Q.98, E.99, A.169, R.172 10 PLIP interactions: 7 interactions with chain B, 3 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 Salt bridges: B:R.172, A:R.690 SO4.24: 3 residues within 4Å: Chain A: K.1062, A.1138, K.1141 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.1062, A:K.1141 SO4.25: 4 residues within 4Å: Chain A: S.1196, G.1198, E.1199, R.1202 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.1196, A:G.1198, A:E.1199 Water bridges: A:S.1196, A:S.1197, A:E.1199 Salt bridges: A:R.1202 SO4.26: 4 residues within 4Å: Chain A: Q.581, V.745, R.746, R.749 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.746 Water bridges: A:Q.581, A:Q.581, A:R.746, A:R.746, A:R.749 Salt bridges: A:R.749 SO4.46: 8 residues within 4Å: Chain A: S.96, Q.98, E.99, A.169, R.172 Chain B: R.690, P.1041, Q.1042 12 PLIP interactions: 5 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:Q.1042, A:S.96, A:S.96 Water bridges: B:R.690, B:R.690, B:Q.1042, A:S.97, A:S.165, A:S.165, A:R.172 Salt bridges: B:R.690, A:R.172 SO4.47: 2 residues within 4Å: Chain B: A.650, R.651 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.651

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

MG.48: 1 residues within 4Å: Ligands: NAD.45 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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