SMTL ID : 9dl3.1 (2 other biounits)

Structure of proline utilization A complexed with quinoline-2-carboxylic acid

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: 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, 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: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:H.425, A:N.426, A:S.499, A:F.501 Water bridges: A:A.423, A:V.502 Salt bridges: A:K.372, A:K.372, A:K.397 pi-Stacking: A:W.376, A:W.376 FAD.21: 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 27 PLIP interactions: 27 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:E.494, B:S.499, B:F.501 Water bridges: 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

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

PGE.2: 7 residues within 4Å: Chain A: H.1047, 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.5: 5 residues within 4Å: Chain A: G.544, D.545, R.547, T.548, R.689 No protein-ligand interaction detected (PLIP) PGE.7: 7 residues within 4Å: Chain A: L.553, N.557, E.559, T.560, S.563, L.564, P.653 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.563, A:S.563 PGE.10: 6 residues within 4Å: Chain A: T.988, S.989, I.991, L.996, T.1097, H.1099 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.1097, A:T.1097 Water bridges: A:A.1100, A:E.1214, A:E.1214 PGE.22: 5 residues within 4Å: Chain B: H.1047, G.1081, L.1082, L.1098, H.1099 No protein-ligand interaction detected (PLIP) PGE.23: 6 residues within 4Å: Chain B: G.544, D.545, A.546, R.547, T.548, R.689 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.545 Water bridges: B:R.689

4 x QNC: quinoline-2-carboxylic acid(Non-covalent)

QNC.3: 7 residues within 4Å: Chain A: D.764, G.765, R.766, E.787, L.791 Ligands: QNC.4, MG.20 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.791 Hydrogen bonds: A:G.765, A:R.766 Water bridges: A:E.735, A:E.735 QNC.4: 9 residues within 4Å: Chain A: I.705, K.732, G.765, G.768, A.769, V.788, L.791, I.792 Ligands: QNC.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.705, A:A.769, A:L.791, A:I.792 Water bridges: A:K.732, A:K.732 Salt bridges: A:K.732 QNC.24: 8 residues within 4Å: Chain B: Y.259, R.365, T.415, D.416, H.442, V.443, G.444, K.445 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.259 Hydrogen bonds: B:T.415 Salt bridges: B:R.365, B:H.442 pi-Cation interactions: B:R.365 QNC.25: 7 residues within 4Å: Chain B: I.705, K.732, G.765, G.768, A.769, V.788, I.792 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.769, B:V.788, B:V.788, B:I.792 Water bridges: B:K.732, B:E.735 Salt bridges: B:K.732

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

PEG.6: 4 residues within 4Å: Chain A: A.639, D.642, R.643, E.646 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.642, A:E.646 PEG.9: 5 residues within 4Å: Chain A: L.385, D.386, I.671, A.672, R.675 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.675 Water bridges: A:A.672, A:D.679 PEG.12: 4 residues within 4Å: Chain A: G.1102, G.1125, S.1127, R.1150 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.1127 Water bridges: A:A.1100, A:S.1127, A:S.1127 PEG.13: 6 residues within 4Å: Chain A: K.1155, D.1156, W.1157, A.1181, A.1184, L.1185 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.1155, A:W.1157 Water bridges: A:A.1158, A:A.1158 PEG.14: 3 residues within 4Å: Chain A: R.1000, N.1001, I.1003 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.1001 Water bridges: A:D.833 PEG.26: 4 residues within 4Å: Chain B: R.382, R.1000, N.1001, I.1003 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.382, B:R.382, B:N.1001 Water bridges: B:R.845, B:R.1000 PEG.27: 6 residues within 4Å: Chain B: L.385, D.386, I.671, A.672, R.675, E.676 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.672, B:R.675 Water bridges: B:A.672, B:D.679 PEG.29: 6 residues within 4Å: Chain B: K.1155, D.1156, W.1157, A.1181, L.1185 Ligands: FMT.34 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.1155, B:W.1157 Water bridges: B:A.1158, B:A.1184 PEG.30: 4 residues within 4Å: Chain B: E.559, T.560, S.563 Ligands: FMT.33 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.563, B:S.563 PEG.31: 3 residues within 4Å: Chain B: G.1125, S.1127, R.1150 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.1127 Water bridges: B:S.1127, B:S.1127

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

FMT.8: 3 residues within 4Å: Chain A: Q.1042, S.1044, L.1084 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.1042, A:S.1044 Water bridges: B:N.162, B:N.162 FMT.11: 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:R.42, A:A.389 Water bridges: A:D.554, A:T.560 FMT.32: 4 residues within 4Å: Chain B: P.349, F.350, D.353, K.410 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.410 FMT.33: 5 residues within 4Å: Chain B: R.42, L.388, A.389, D.554 Ligands: PEG.30 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.389 Water bridges: B:D.554, B:N.557, B:T.560 FMT.34: 2 residues within 4Å: Chain B: R.1174 Ligands: PEG.29 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.1174 Water bridges: B:R.1174

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

SO4.15: 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 SO4.16: 4 residues within 4Å: Chain A: K.1062, A.1138, K.1141, N.1142 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.1062 SO4.17: 7 residues within 4Å: Chain A: F.710, R.845, S.847, I.1003, G.1004, A.1005, F.1012 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:C.846, A:S.847, A:S.847, A:S.847, A:G.1004, A:A.1005 Salt bridges: A:R.845 SO4.18: 4 residues within 4Å: Chain A: R.71, S.511, I.512, D.513 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.512, A:D.513 Water bridges: A:R.71, A:R.78 Salt bridges: A:R.71 SO4.19: 5 residues within 4Å: Chain A: 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 SO4.35: 2 residues within 4Å: Chain B: A.650, R.651 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.651, B:R.651 Salt bridges: B:R.651 SO4.36: 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: 6 interactions with chain B, 4 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, A:R.690 Salt bridges: B:R.172, A:R.690 SO4.37: 7 residues within 4Å: Chain B: F.710, R.845, S.847, I.1003, G.1004, A.1005, F.1012 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:C.846, B:S.847, B:S.847, B:G.1004, B:A.1005 Salt bridges: B:R.845 SO4.38: 4 residues within 4Å: Chain B: R.71, S.511, I.512, D.513 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.512, B:D.513 Salt bridges: B:R.71 SO4.39: 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 SO4.40: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.234

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

MG.20: 1 residues within 4Å: Ligands: QNC.3 No protein-ligand interaction detected (PLIP)

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

PG4.28: 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:N.896

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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