SMTL ID : 9dl8.3 (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

monomer

Ligands

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

FAD.1: 30 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 Ligands: 01.8 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:A.423, A:Q.449, A:Y.475, 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:S.499, A:F.501 Water bridges: A:K.397, 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

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

PEG.2: 5 residues within 4Å: Chain A: D.1131, A.1133, W.1157, R.1174, A.1177 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.1131, A:R.1174, A:R.1174 PEG.4: 4 residues within 4Å: Chain A: Y.239, R.240, P.289, R.290 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.290 PEG.5: 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.6: 4 residues within 4Å: Chain A: S.1196, S.1197, G.1198, R.1202 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.1196, A:G.1198, A:R.1202, A:R.1202 Water bridges: A:S.1196, A:S.1197, A:S.1197 PEG.7: 5 residues within 4Å: Chain A: G.1102, G.1125, S.1127, L.1149, R.1150 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.1127, A:S.1127 PEG.9: 5 residues within 4Å: Chain A: L.553, T.560, S.563, L.564, P.653 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.563 Water bridges: A:E.559, A:T.560, A:A.567 PEG.11: 5 residues within 4Å: Chain A: T.988, T.1097, H.1099, V.1216, I.1220 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.1099 PEG.16: 4 residues within 4Å: Chain A: Y.434, H.435, G.438, K.439 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.435 PEG.18: 9 residues within 4Å: Chain A: A.1070, A.1074, H.1116, A.1119, A.1120, P.1204, D.1205, Y.1207, L.1209 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.1116, A:D.1205, A:D.1205

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

PGE.3: 6 residues within 4Å: Chain A: H.1047, G.1081, L.1082, D.1083, L.1098, H.1099 No protein-ligand interaction detected (PLIP) PGE.14: 10 residues within 4Å: Chain A: 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 A Hydrogen bonds: A:L.553, A:R.675, A:D.679 Water bridges: A:N.549, A:R.675, A:D.679

1 x 01: (4-methoxyphenyl)methanol

01.8: 9 residues within 4Å: Chain A: K.267, D.308, A.309, A.374, Y.375, L.451, Y.475, R.491 Ligands: FAD.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.374, A:Y.475 Hydrogen bonds: A:Y.375

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

PG4.10: 4 residues within 4Å: Chain A: R.790, A.1183, A.1184, L.1185 No protein-ligand interaction detected (PLIP) PG4.12: 2 residues within 4Å: Chain A: N.896, K.899 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.896, A:K.899

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

FMT.13: 6 residues within 4Å: Chain A: N.896, R.941, E.942, V.943, F.944 Ligands: NAD.19 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.942, A:F.944 FMT.15: 4 residues within 4Å: Chain A: R.42, L.388, A.389, D.554 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.389 Water bridges: A:D.554, A:N.557, A:T.560 FMT.17: 2 residues within 4Å: Chain A: S.94, L.95 No protein-ligand interaction detected (PLIP)

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

NAD.19: 26 residues within 4Å: Chain A: 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.13, MG.22 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:P.707 Hydrogen bonds: A:S.706, A:N.709, A:K.732, A:G.784, A:S.785, A:E.812 Water bridges: A:E.735, A:E.735, A:E.735, A:E.736, A:S.785, A:N.896, A:F.944 pi-Stacking: A:F.944

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

SO4.20: 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 SO4.21: 2 residues within 4Å: Chain A: A.650, R.651 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.651

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

MG.22: 1 residues within 4Å: Ligands: NAD.19 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

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