SMTL ID : 9dl6.1 (2 other biounits)

Structure of proline utilization A complexed with piperidine-3-carboxylic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.42 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, A.423, T.424, H.425, N.426, Q.449, C.450, L.451, Y.475, E.494, N.495, S.499, S.500, F.501, I.1234, G.1235 32 PLIP interactions: 32 interactions with chain A Hydrophobic interactions: A:A.423, A:Q.449, A:L.451, 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:K.397, A:T.400, A:T.424, A:H.425, A:N.426, A:N.426, A:E.494, A:S.499, A:F.501 Water bridges: A:E.494, A:N.495, A:V.502 Salt bridges: A:K.372, A:K.372, A:K.397 pi-Stacking: A:W.376, A:W.376 FAD.21: 31 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, I.1234, G.1235 33 PLIP interactions: 33 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:N.426, B:E.494, B:E.494, B:E.494, B:S.499, B:F.501, B:G.1235 Water bridges: B:A.423, 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

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

PEG.2: 5 residues within 4Å: Chain A: Y.239, P.289, R.290, A.293 Ligands: FMT.7 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.290, A:R.290 PEG.4: 6 residues within 4Å: Chain A: A.1100, G.1102, G.1125, S.1127, L.1149, R.1150 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.1150 PEG.5: 4 residues within 4Å: Chain A: Y.434, H.435, G.438, K.439 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.438 Water bridges: A:Y.434, A:R.470 PEG.9: 6 residues within 4Å: Chain A: G.544, D.545, A.546, 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.23: 5 residues within 4Å: Chain B: G.544, D.545, R.547, T.548, R.689 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.544 Water bridges: B:R.689, B:R.689 PEG.25: 4 residues within 4Å: Chain B: R.805, S.1196, S.1197, G.1198 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.805, B:R.805, B:S.1196, B:G.1198 Water bridges: B:S.1197, B:S.1197 PEG.28: 4 residues within 4Å: Chain B: R.282, H.871, E.872, L.873 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.282, B:L.873, B:H.874

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

PGE.3: 8 residues within 4Å: Chain A: I.984, T.988, L.996, L.1095, T.1097, H.1099, A.1218, I.1220 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.988 PGE.10: 6 residues within 4Å: Chain A: L.1080, G.1081, L.1082, T.1097, L.1098, H.1099 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.1083 PGE.22: 6 residues within 4Å: Chain B: H.1047, L.1080, G.1081, L.1082, L.1098, H.1099 No protein-ligand interaction detected (PLIP) PGE.27: 5 residues within 4Å: Chain B: D.1156, W.1157, R.1174, A.1177, A.1181 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:W.1157, B:R.1174, B:A.1177 Water bridges: B:A.1158, B:R.1174, B:A.1181

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

FMT.6: 5 residues within 4Å: Chain A: G.1021, P.1022, R.1101, E.1214, E.1215 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.1101, A:E.1215, A:E.1215, A:E.1215 Water bridges: A:R.1101 FMT.7: 3 residues within 4Å: Chain A: E.236, Y.239 Ligands: PEG.2 No protein-ligand interaction detected (PLIP) FMT.8: 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.20: 1 residues within 4Å: Chain A: T.864 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.864 FMT.26: 6 residues within 4Å: Chain B: G.1021, P.1022, R.1101, V.1213, E.1214, E.1215 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.1101, B:E.1215 Water bridges: B:G.1014, B:E.1214 FMT.29: 4 residues within 4Å: Chain B: R.42, L.388, A.389, D.554 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.389 Water bridges: B:R.42, B:D.554, B:N.557, B:T.560

2 x 01: (3S)-piperidine-3-carboxylic acid

01.11: 11 residues within 4Å: Chain A: E.676, F.710, I.714, R.845, C.846, S.847, I.1003, G.1004, A.1005, F.1012 Ligands: ID7.12 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.710, A:F.710, A:I.714, A:F.1012 Hydrogen bonds: A:S.847, A:G.1004, A:A.1005 Salt bridges: A:R.845 01.30: 11 residues within 4Å: Chain B: E.676, F.710, I.714, R.845, C.846, S.847, I.1003, G.1004, A.1005, F.1012 Ligands: ID7.31 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.710, B:F.710, B:I.714, B:F.1012, B:F.1012 Hydrogen bonds: B:E.676, B:S.847, B:G.1004, B:A.1005 Salt bridges: B:R.845

2 x ID7: (3R)-piperidine-3-carboxylic acid(Non-covalent)

ID7.12: 11 residues within 4Å: Chain A: E.676, F.710, I.714, R.845, C.846, S.847, I.1003, G.1004, A.1005, F.1012 Ligands: 01.11 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.710, A:F.710, A:I.714, A:F.1012 Hydrogen bonds: A:S.847, A:G.1004, A:A.1005 Water bridges: A:E.676 Salt bridges: A:R.845 ID7.31: 11 residues within 4Å: Chain B: E.676, F.710, I.714, R.845, C.846, S.847, I.1003, G.1004, A.1005, F.1012 Ligands: 01.30 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.710, B:F.710, B:I.714, B:F.1012 Hydrogen bonds: B:E.676, B:S.847, B:G.1004, B:A.1005 Salt bridges: B:R.845

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

SO4.13: 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: 7 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.96, B:E.99, 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 SO4.14: 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 SO4.15: 4 residues within 4Å: Chain A: S.1196, G.1198, E.1199, R.1202 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.1196, A:G.1198, A:E.1199 Salt bridges: A:R.1202 SO4.16: 4 residues within 4Å: Chain A: K.1062, A.1138, K.1141, N.1142 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.1141 Salt bridges: A:K.1062 SO4.17: 4 residues within 4Å: Chain A: T.158, S.159, R.1093, A.1229 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.159, A:S.159 Water bridges: A:A.1229, A:A.1229 Salt bridges: A:R.1093 SO4.32: 8 residues within 4Å: Chain A: S.96, Q.98, E.99, A.169, R.172 Chain B: R.690, P.1041, Q.1042 11 PLIP interactions: 4 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:Q.1042, A:S.97, A:S.165, A:S.165, A:R.172 Salt bridges: B:R.690, A:R.172 SO4.33: 4 residues within 4Å: Chain B: R.71, S.511, I.512, D.513 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.512, B:D.513 Water bridges: B:R.78 Salt bridges: B:R.71

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

NAD.18: 31 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, I.792, E.812, T.813, G.814, C.846, E.942, F.944, L.972, F.1012, S.1018 Ligands: MG.19 18 PLIP interactions: 18 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.736, A:T.786, A:T.813, A:E.942, A:E.942, A:E.942 NAD.34: 32 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, L.972, F.1012, S.1018 Ligands: MG.35 17 PLIP interactions: 17 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.736, B:T.786, B:L.791, B:T.813, B:E.942

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

MG.19: 1 residues within 4Å: Ligands: NAD.18 No protein-ligand interaction detected (PLIP) MG.35: 1 residues within 4Å: Ligands: NAD.34 No protein-ligand interaction detected (PLIP)

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

PG4.24: 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

Related Entries With Identical Sequence