SMTL ID : 7myb.2 (2 other biounits)

Structure of proline utilization A with tetrahydrothiophene-2-carboxylate bound in the proline dehydrogenase active site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

monomer

Ligands

1 x UJM: (2S)-thiolane-2-carboxylic acid(Non-covalent)

UJM.1: 7 residues within 4Å: Chain A: K.267, D.308, A.374, Y.475, R.490 Ligands: UJP.2, FAD.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.475 Salt bridges: A:K.267, A:R.490

1 x UJP: (2R)-thiolane-2-carboxylic acid(Non-covalent)

UJP.2: 7 residues within 4Å: Chain A: K.267, D.308, A.374, Y.475, R.490 Ligands: UJM.1, FAD.4 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.267, A:R.490

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

PGE.3: 5 residues within 4Å: Chain A: H.1047, L.1080, G.1081, L.1098, H.1099 No protein-ligand interaction detected (PLIP)

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

FAD.4: 33 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, 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, I.1234 Ligands: UJM.1, UJP.2 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:A.423, A:Q.449, A:L.451, A:L.451, 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:D.401, A:H.425, A:N.426, A:E.494, A:E.494, A:S.499, A:F.501 Water bridges: A:K.397, A:V.502 Salt bridges: A:K.372, A:K.372, A:K.397 pi-Stacking: A:W.376, A:W.376, A:W.376

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

NAD.5: 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, L.791, I.792, E.812, T.813, G.814, C.846, E.942, F.944, F.1012, S.1018 Ligands: MG.7 19 PLIP interactions: 19 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.735, A:E.736, A:E.736, A:G.765, A:T.786, A:Q.795, A:T.813, A:E.942

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

SO4.6: 3 residues within 4Å: Chain A: R.690, P.1041, Q.1042 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.1042 Water bridges: A:R.690, A:R.690, A:Q.1042, A:Q.1042 Salt bridges: A:R.690

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

MG.7: 1 residues within 4Å: Ligands: NAD.5 No protein-ligand interaction detected (PLIP)

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

PEG.8: 8 residues within 4Å: Chain A: A.672, E.673, E.676, F.710, A.713, I.714, R.845, A.1005 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.845 Water bridges: A:I.1003

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
B

Bifunctional protein PutA

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