SMTL ID : 7mya.1 (2 other biounits)

Structure of proline utilization A with the FAD covalently-modified by 1,3-dithiolane

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

monomer

Ligands

1 x UJJ: [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-[5-(1,3-dithiolan-2-yl)-7,8-dimethyl-2,4-dioxo-1,3,4,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate(Non-covalent)

UJJ.1: 33 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, R.491, E.494, S.499, S.500, F.501, G.1235 35 PLIP interactions: 35 interactions with chain A Hydrophobic interactions: A:A.423, A:Q.449, A:L.451, A:L.451, A:Y.475, A:Y.475 Hydrogen bonds: A:D.308, A:A.309, A:A.309, A:Q.342, A:K.372, A:G.373, A:G.373, A:G.373, A:A.374, A:T.395, A:T.400, A:T.424, A:H.425, A:H.425, A:N.426, A:N.426, A:E.494, A:E.494, A:S.499, A:F.501, A:G.1235 Water bridges: A:K.397, A:A.423 Salt bridges: A:K.372, A:K.372, A:K.397, A:H.425 pi-Stacking: A:W.376, A:W.376

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

MG.2: 1 residues within 4Å: Ligands: NAD.3 No protein-ligand interaction detected (PLIP)

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

NAD.3: 30 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, F.1012, S.1018 Ligands: MG.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: 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

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

SO4.4: 3 residues within 4Å: Chain A: R.690, P.1041, Q.1042 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.1042 Water bridges: A:R.690, A:R.690, A:Q.1042 Salt bridges: A:R.690 SO4.5: 4 residues within 4Å: Chain A: R.71, S.511, I.512, D.513 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.512, A:D.513 Water bridges: A:E.75 Salt bridges: A:R.71 SO4.6: 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 SO4.7: 2 residues within 4Å: Chain A: K.1062, A.1138 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.1138 Salt bridges: A:K.1062 SO4.8: 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

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

PGE.9: 5 residues within 4Å: Chain A: H.1047, L.1080, G.1081, L.1098, H.1099 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.1047

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Campbell, A.C. et al., Photoinduced Covalent Irreversible Inactivation of Proline Dehydrogenase by S-Heterocycles. Acs Chem.Biol. (2021)

Release Date

2021-09-29

Peptides

Bifunctional protein PutA: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Bifunctional protein PutA

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