SMTL ID : 9dl4.1 (2 other biounits)

Structure of proline utilization A complexed with 2-pyridinethiol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

PGE.1: 5 residues within 4Å: Chain A: L.1080, G.1081, D.1083, L.1098, H.1099 No protein-ligand interaction detected (PLIP) PGE.14: 4 residues within 4Å: Chain B: L.1080, G.1081, L.1098, H.1099 No protein-ligand interaction detected (PLIP)

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

PEG.2: 3 residues within 4Å: Chain A: Y.239, P.289, R.290 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.290 Water bridges: A:R.290 PEG.4: 7 residues within 4Å: Chain A: K.381, L.385, R.1000, E.1092, N.1221, A.1223 Ligands: PEG.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.381, A:N.1221 Water bridges: A:N.1221, A:A.1223 PEG.5: 5 residues within 4Å: Chain A: R.382, R.1000, N.1001, I.1003 Ligands: PEG.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.382, A:N.1001 Water bridges: A:R.845, A:R.845 PEG.6: 4 residues within 4Å: Chain A: G.1102, G.1125, S.1127, R.1150 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.1127 Water bridges: A:R.1103 PEG.8: 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 Hydrogen bonds: A:T.548 Water bridges: A:G.544, A:T.548, A:D.642, A:R.689 PEG.15: 6 residues within 4Å: Chain B: K.381, L.385, R.1000, E.1092, N.1221, A.1223 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.381, B:E.1092, B:N.1221 Water bridges: B:N.1221 PEG.17: 6 residues within 4Å: Chain B: G.544, D.545, A.546, R.547, T.548, R.689 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.544 PEG.18: 3 residues within 4Å: Chain B: R.805, S.1196, G.1198 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.805, B:R.805, B:S.1196, B:G.1198

2 x PYS: 2-PYRIDINETHIOL(Non-covalent)

PYS.3: 7 residues within 4Å: Chain A: I.705, G.765, G.768, A.769, V.788, I.792, Q.795 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.769, A:I.792 PYS.16: 7 residues within 4Å: Chain B: I.705, G.765, G.768, A.769, V.788, I.792, Q.795 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.769, B:I.792

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

FMT.7: 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:R.42, A:A.389 Water bridges: A:D.554, A:D.554, A:T.560 FMT.19: 4 residues within 4Å: Chain B: L.553, S.563, L.564, P.653 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.563 FMT.20: 1 residues within 4Å: Chain B: R.1174 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.1174, B:R.1174

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

SO4.9: 7 residues within 4Å: Chain A: R.690, P.1041, Q.1042 Chain B: S.96, Q.98, A.169, R.172 9 PLIP interactions: 6 interactions with chain B, 3 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 Salt bridges: B:R.172, A:R.690 SO4.10: 6 residues within 4Å: Chain A: S.139, Q.855, E.856, D.857, R.954, R.955 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.855, A:E.856, A:D.857, A:R.955 Water bridges: A:D.956 Salt bridges: A:R.954 SO4.11: 3 residues within 4Å: Chain A: S.1196, G.1198, R.1202 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.1196, A:G.1198 Salt bridges: A:R.1202 SO4.12: 2 residues within 4Å: Chain A: K.1062, K.1141 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.1062 SO4.21: 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 SO4.22: 5 residues within 4Å: Chain B: Q.855, E.856, D.857, R.954, R.955 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.855, B:D.857, B:R.955 Water bridges: B:D.956

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

FAD.13: 28 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, S.499, S.500, F.501 27 PLIP interactions: 27 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 Salt bridges: A:K.372, A:K.372, A:K.397 pi-Stacking: A:W.376, A:W.376 FAD.23: 28 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, S.499, S.500, F.501 24 PLIP interactions: 24 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:K.397, B:H.425, B:N.426, B:S.499, B:F.501 Water bridges: B:K.372, B:K.372 Salt bridges: B:K.372, B:K.372, B:K.397 pi-Stacking: B:W.376, B:W.376

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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