SMTL ID : 9dl5.3 (2 other biounits)

Structure of proline utilization A complexed with 5-chloro-1-indanone

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 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: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

5 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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.1131, A:R.1174, A:R.1174 Water bridges: A:A.1177, A:A.1181 PEG.4: 4 residues within 4Å: Chain A: N.896, K.899, R.941 Ligands: FMT.12 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.896, A:K.899 Water bridges: A:K.899, A:R.941, A:R.941 PEG.5: 4 residues within 4Å: Chain A: E.236, Y.239, R.240, R.290 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.290, A:R.290 PEG.8: 6 residues within 4Å: Chain A: L.553, T.560, S.563, L.564, A.567, P.653 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.563 Water bridges: A:A.567 PEG.11: 4 residues within 4Å: Chain A: S.1196, S.1197, G.1198, R.1202 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.805, A:S.1196, A:G.1198, A:R.1202 Water bridges: A:S.1197, A:S.1197

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

PGE.3: 5 residues within 4Å: Chain A: H.1047, G.1081, L.1082, L.1098, H.1099 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.1083 Water bridges: A:D.1083, A:H.1099

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

PG4.6: 8 residues within 4Å: Chain A: G.544, D.545, A.546, R.547, T.548, E.686, R.689, R.690 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.544, A:E.686 Water bridges: A:R.689, A:R.689

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

FMT.7: 2 residues within 4Å: Chain A: A.39, R.43 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.39, A:R.43 FMT.9: 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.10: 4 residues within 4Å: Chain A: S.1045, V.1046, G.1081, L.1082 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.1046, A:D.1083 Water bridges: A:S.1044 FMT.12: 2 residues within 4Å: Chain A: K.899 Ligands: PEG.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.899

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

SO4.13: 2 residues within 4Å: Chain A: A.650, R.651 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.651 SO4.14: 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 SO4.15: 1 residues within 4Å: Chain A: R.204 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.204 SO4.16: 3 residues within 4Å: Chain A: D.764, G.765, R.766 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.735, A:G.765, A:R.766 SO4.17: 7 residues within 4Å: Chain A: L.385, D.386, L.668, I.671, A.672, R.675 Ligands: SO4.19 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.386, A:A.672 Water bridges: A:R.382 Salt bridges: A:R.675 SO4.18: 7 residues within 4Å: Chain A: F.710, R.845, S.847, I.1003, G.1004, A.1005, F.1012 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.847, A:S.847, A:G.1004, A:A.1005 Water bridges: A:R.845 Salt bridges: A:R.845 SO4.19: 5 residues within 4Å: Chain A: A.672, R.675, E.676, D.679 Ligands: SO4.17 7 PLIP interactions: 7 interactions with chain A Water bridges: A:R.675, A:R.675, A:R.675, A:D.679, A:D.679, A:G.1004 Salt bridges: A:R.675 SO4.20: 2 residues within 4Å: Chain A: R.240, E.243 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.240, A:R.240 Salt bridges: A:R.240 SO4.21: 5 residues within 4Å: Chain A: Q.855, E.856, D.857, R.954, R.955 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.855, A:D.857, A:R.955 Water bridges: A:D.956 SO4.22: 4 residues within 4Å: Chain A: R.71, S.511, I.512, D.513 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.512, A:D.513 Salt bridges: A:R.71

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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