SMTL ID : 9dl5.1 (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

homo-dimer

Ligands

2 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, D.401, A.423, T.424, H.425, N.426, Q.449, C.450, L.451, Y.475, S.499, S.500, F.501 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:S.499, A:F.501 Water bridges: A:V.502 Salt bridges: A:K.372, A:K.372, A:K.397 pi-Stacking: A:W.376, A:W.376, A:Y.475 FAD.20: 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: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

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

PGE.2: 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.5: 4 residues within 4Å: Chain A: A.639, D.642, R.643, E.646 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.643 Water bridges: A:R.643 PGE.22: 5 residues within 4Å: Chain B: H.1047, G.1081, L.1082, L.1098, H.1099 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.1083 Water bridges: B:D.1083, B:H.1099

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

FMT.3: 3 residues within 4Å: Chain A: L.327, D.328, G.329 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.329 Water bridges: A:D.330 FMT.9: 4 residues within 4Å: Chain A: E.541, L.542, F.543, G.544 2 PLIP interactions: 2 interactions with chain A Water bridges: A:L.542, A:D.545 FMT.26: 2 residues within 4Å: Chain B: A.39, R.43 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.39, B:R.43 FMT.28: 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.29: 4 residues within 4Å: Chain B: S.1045, V.1046, G.1081, L.1082 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:N.162, A:N.162 Hydrogen bonds: B:V.1046, B:D.1083 FMT.31: 2 residues within 4Å: Chain B: K.899 Ligands: PEG.23 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.899

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

PEG.4: 4 residues within 4Å: Chain A: E.236, Y.239, P.289, R.290 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.236 Water bridges: A:E.236, A:R.290, A:R.290 PEG.7: 4 residues within 4Å: Chain A: K.575, W.576, R.651, R.746 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.575, A:R.651 PEG.10: 5 residues within 4Å: Chain A: T.560, S.563, L.564, A.567, P.653 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.567, A:T.654 PEG.21: 5 residues within 4Å: Chain B: D.1131, A.1133, W.1157, R.1174, A.1177 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.1131, B:R.1174, B:R.1174 Water bridges: B:A.1177, B:A.1181 PEG.23: 4 residues within 4Å: Chain B: N.896, K.899, R.941 Ligands: FMT.31 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.896, B:K.899 Water bridges: B:K.899, B:R.941, B:R.941 PEG.24: 4 residues within 4Å: Chain B: E.236, Y.239, R.240, R.290 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.290, B:R.290 PEG.27: 6 residues within 4Å: Chain B: L.553, T.560, S.563, L.564, A.567, P.653 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.563 Water bridges: B:A.567 PEG.30: 4 residues within 4Å: Chain B: S.1196, S.1197, G.1198, R.1202 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.805, B:S.1196, B:G.1198, B:R.1202 Water bridges: B:S.1197, B:S.1197

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

PG4.6: 7 residues within 4Å: Chain A: D.545, R.547, T.548, E.686, R.689, R.690 Chain B: S.94 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.686 Water bridges: A:T.548, A:T.548, A:R.689, A:R.689, A:R.690 PG4.25: 9 residues within 4Å: Chain A: S.94 Chain B: G.544, D.545, A.546, R.547, T.548, E.686, R.689, R.690 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Water bridges: A:S.94, B:R.689, B:R.689, B:R.690 Hydrogen bonds: B:G.544, B:E.686

1 x 01: 5-chloro-2,3-dihydro-1H-inden-1-one

01.8: 8 residues within 4Å: Chain A: I.705, G.765, G.768, A.769, V.788, L.791, I.792, Q.795 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.705, A:V.788, A:V.788, A:I.792

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

SO4.11: 5 residues within 4Å: Chain A: Q.855, E.856, D.857, R.954, R.955 Ligand excluded by PLIP SO4.12: 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 SO4.13: 2 residues within 4Å: Chain A: S.332, G.333 Ligand excluded by PLIP SO4.14: 7 residues within 4Å: Chain A: F.710, R.845, S.847, I.1003, G.1004, A.1005, F.1012 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain A: S.1196, G.1198, R.1202 Ligand excluded by PLIP SO4.16: 7 residues within 4Å: Chain A: L.385, D.386, L.668, I.671, A.672, R.675 Ligands: SO4.19 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain A: K.1155, D.1156, W.1157 Ligand excluded by PLIP SO4.18: 4 residues within 4Å: Chain A: R.71, S.511, I.512, D.513 Ligand excluded by PLIP SO4.19: 4 residues within 4Å: Chain A: A.672, R.675, D.679 Ligands: SO4.16 Ligand excluded by PLIP SO4.32: 2 residues within 4Å: Chain B: A.650, R.651 Ligand excluded by PLIP SO4.33: 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 SO4.34: 1 residues within 4Å: Chain B: R.204 Ligand excluded by PLIP SO4.35: 3 residues within 4Å: Chain B: D.764, G.765, R.766 Ligand excluded by PLIP SO4.36: 7 residues within 4Å: Chain B: L.385, D.386, L.668, I.671, A.672, R.675 Ligands: SO4.38 Ligand excluded by PLIP SO4.37: 7 residues within 4Å: Chain B: F.710, R.845, S.847, I.1003, G.1004, A.1005, F.1012 Ligand excluded by PLIP SO4.38: 5 residues within 4Å: Chain B: A.672, R.675, E.676, D.679 Ligands: SO4.36 Ligand excluded by PLIP SO4.39: 2 residues within 4Å: Chain B: R.240, E.243 Ligand excluded by PLIP SO4.40: 5 residues within 4Å: Chain B: Q.855, E.856, D.857, R.954, R.955 Ligand excluded by PLIP SO4.41: 5 residues within 4Å: Chain A: P.527 Chain B: R.71, S.511, I.512, D.513 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

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