SMTL ID : 9dl9.1 (2 other biounits)

Structure of proline utilization A co-crystallized with 4-methoxybenzyl alcohol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.32 Å

Oligo State

homo-dimer

Ligands

2 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, D.401, A.423, T.424, H.425, N.426, Q.449, C.450, L.451, Y.475, S.499, S.500, F.501, I.1234, G.1235 Ligands: 01.2 29 PLIP interactions: 29 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:S.499, A:F.501 Water bridges: A:A.423 Salt bridges: A:K.372, A:K.372, A:K.397 pi-Stacking: A:W.376, A:W.376 FAD.13: 33 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, 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, I.1234, G.1235 Ligands: 01.16 29 PLIP interactions: 29 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: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:E.494, B:S.499, B:F.501, B:G.1235 Water bridges: 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, B:W.376

3 x 01: (4-methoxyphenyl)methanol

01.2: 8 residues within 4Å: Chain A: K.267, D.308, A.309, A.374, Y.375, L.451, Y.475 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 01.14: 7 residues within 4Å: Chain B: A.672, E.673, E.676, F.710, A.713, I.714, R.845 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:E.676, B:A.713 Hydrogen bonds: B:N.669, B:R.845 Water bridges: B:S.841 pi-Stacking: B:F.710 01.16: 8 residues within 4Å: Chain B: K.267, D.308, A.309, A.374, Y.375, L.451, Y.475 Ligands: FAD.13 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.3: 4 residues within 4Å: Chain A: L.1080, G.1081, L.1098, H.1099 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.1083 PGE.17: 5 residues within 4Å: Chain B: L.1080, G.1081, L.1082, L.1098, H.1099 No protein-ligand interaction detected (PLIP) PGE.21: 6 residues within 4Å: Chain B: G.544, D.545, A.546, R.547, T.548, R.689 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.544 Water bridges: B:E.686, B:R.689, B:R.689, A:S.94

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

FMT.4: 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:D.554, A:T.560 FMT.18: 4 residues within 4Å: Chain A: R.176 Chain B: P.634, L.692, G.693 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.692 Water bridges: B:S.635 FMT.19: 6 residues within 4Å: Chain B: G.1021, P.1022, R.1101, V.1213, E.1214, E.1215 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.1101, B:E.1215, B:E.1215 FMT.20: 4 residues within 4Å: Chain B: R.42, L.388, A.389, D.554 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.389 Water bridges: B:D.554, B:T.560

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

PEG.5: 4 residues within 4Å: Chain A: Y.239, P.289, R.290, A.293 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.290 Water bridges: A:R.290 PEG.6: 6 residues within 4Å: Chain A: G.544, D.545, A.546, R.547, T.548, R.689 5 PLIP interactions: 5 interactions with chain A Water bridges: A:T.548, A:E.686, A:R.689, A:R.689, A:R.689 PEG.15: 5 residues within 4Å: Chain B: R.805, S.1196, S.1197, G.1198, R.1202 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.805, B:R.805, B:S.1196, B:G.1198, B:R.1202, B:R.1202 Water bridges: B:S.1197, B:S.1197

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

NAD.7: 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.12 24 PLIP interactions: 24 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.735, A:E.736, A:E.736, A:E.736, A:E.736, A:S.785, A:S.785, A:T.786, A:Q.795, A:T.813, A:E.942, A:E.942 NAD.23: 30 residues within 4Å: Chain B: 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, F.1012 Ligands: MG.25 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:P.707, B:F.710, B:I.714, B:T.783 Hydrogen bonds: B:S.706, B:S.706, B:W.708, B:K.732, B:E.735, B:S.785, B:T.813, B:E.942 Water bridges: B:E.735, B:E.736, B:E.736, B:G.765, B:T.786, B:Q.795, B:T.813, B:E.942

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

SO4.8: 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: 6 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:S.96, A:Q.1042 Water bridges: B:S.96, B:S.97, B:R.172, B:R.172, A:R.690, A:R.690 Salt bridges: B:R.172, A:R.690 SO4.9: 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 SO4.10: 4 residues within 4Å: Chain A: K.1062, A.1138, K.1141, N.1142 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.1062 SO4.11: 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:S.1196, A:G.1198, A:E.1199 Water bridges: A:S.1197, A:R.1202 Salt bridges: A:R.1202 SO4.24: 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: 7 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:S.96, A:S.96, B:Q.1042 Water bridges: A:S.97, A:S.165, A:S.165, A:R.172, B:R.690, B:Q.1042, B:Q.1042 Salt bridges: A:R.172, B:R.690

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

MG.12: 1 residues within 4Å: Ligands: NAD.7 No protein-ligand interaction detected (PLIP) MG.25: 1 residues within 4Å: Ligands: NAD.23 No protein-ligand interaction detected (PLIP)

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.22: 3 residues within 4Å: Chain B: N.896, K.899, R.941 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.899 Water bridges: B:R.941

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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