SMTL ID : 9e5w.1 (2 other biounits)

Proline utilization A (PutA) from Sinorhizobium meliloti inactivated by N-propargylglycine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

homo-dimer

Ligands

2 x P5F: N-propargylglycine-modified flavin adenine dinucleotide(Covalent)

P5F.1: 30 residues within 4Å: Chain A: K.267, 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 34 PLIP interactions: 34 interactions with chain A Hydrophobic interactions: A:K.267, A:D.308, A:A.423, A:Q.449, A:L.451, A:Y.475, A:Y.475 Hydrogen bonds: A:D.308, 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:N.426, A:S.499, A:F.501 Water bridges: A:K.267 Salt bridges: A:K.372, A:K.372, A:K.397 pi-Stacking: A:W.376, A:W.376 P5F.12: 31 residues within 4Å: Chain B: K.267, 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, E.494, S.499, S.500, F.501 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: B:K.267, B:D.308, B:A.423, B:Q.449, B:L.451, B:Y.475, 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:K.397, B:D.401, B:H.425, B:N.426, B:N.426, B:S.499, B:F.501 Water bridges: B:K.267 Salt bridges: B:K.372, B:K.372, B:K.397 pi-Stacking: B:W.376, B:W.376

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

NAD.2: 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.8 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:E.736, A:S.785, A:S.785, A:T.786, A:T.813 NAD.13: 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.16 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.735, B:E.736, B:E.736, B:T.786, B:T.813

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

SO4.3: 8 residues within 4Å: Chain A: R.690, P.1041, Q.1042 Chain B: S.96, Q.98, E.99, A.169, R.172 11 PLIP interactions: 6 interactions with chain B, 5 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, A:Q.1042 Salt bridges: B:R.172, A:R.690 SO4.4: 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 SO4.5: 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 SO4.6: 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 SO4.7: 2 residues within 4Å: Chain A: T.202, R.204 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.202 Water bridges: A:R.204 SO4.14: 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: 7 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:S.96, A:S.96, B:Q.1042 Water bridges: A:S.97, A:S.165, A:S.165, A:R.172, B:R.690, B:R.690, B:Q.1042 Salt bridges: A:R.172, B:R.690 SO4.15: 1 residues within 4Å: Chain B: R.204 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.204

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

MG.8: 1 residues within 4Å: Ligands: NAD.2 No protein-ligand interaction detected (PLIP) MG.16: 1 residues within 4Å: Ligands: NAD.13 No protein-ligand interaction detected (PLIP)

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

FMT.9: 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.17: 4 residues within 4Å: Chain B: R.42, L.388, A.389, D.554 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.389 Water bridges: B:D.554, B:N.557, B:T.560

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

PEG.10: 4 residues within 4Å: Chain A: L.1080, G.1081, L.1098, H.1099 No protein-ligand interaction detected (PLIP) PEG.11: 4 residues within 4Å: Chain A: Y.239, P.289, R.290, A.293 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.290 PEG.18: 5 residues within 4Å: Chain B: R.805, S.1196, S.1197, G.1198, R.1202 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.805, B:R.805, B:S.1196, B:G.1198, B:R.1202, B:R.1202 Water bridges: B:S.1197

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

PG4.19: 7 residues within 4Å: Chain B: H.1047, L.1080, G.1081, L.1082, D.1083, L.1098, H.1099 No protein-ligand interaction detected (PLIP)

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

PGE.20: 3 residues within 4Å: Chain B: N.896, K.899, R.941 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.899

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meeks, K.R. et al., Biochemical, structural, and cellular characterization of S-but-3-yn-2-ylglycine as a mechanism-based covalent inactivator of the flavoenzyme proline dehydrogenase. Arch.Biochem.Biophys. (2025)

Release Date

2025-02-05

Peptides

Bifunctional protein PutA: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Bifunctional protein PutA

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