SMTL ID : 7myc.3 (2 other biounits)

Structure of proline utilization A with the FAD covalently modified by tetrahydrothiophene

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

UJG.1: 32 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.490, S.499, S.500, F.501, I.1234 32 PLIP interactions: 32 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: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:T.424, A:H.425, A:H.425, A:N.426, A:N.426, A:S.499, A:F.501 Salt bridges: A:K.372, A:K.372, A:K.397 pi-Stacking: A:W.376, A:W.376 UJG.12: 30 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, S.499, S.500, F.501 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: 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:T.424, B:H.425, B:N.426, B:N.426, B:S.499, B:F.501 Water bridges: B:K.397 Salt bridges: B:K.372, B:K.372, B:K.397 pi-Stacking: B:W.376, B:W.376

2 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.2: 24 residues within 4Å: Chain A: I.705, S.706, P.707, W.708, N.709, 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, E.812, T.813, G.814, C.846, E.942, F.944 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:P.707 Hydrogen bonds: A:S.706, A:N.709, A:K.732, A:E.735, A:G.784, A:S.785, A:E.812, A:C.846, A:E.942 Water bridges: A:N.896, A:F.944 NAI.14: 25 residues within 4Å: Chain B: I.705, S.706, P.707, W.708, N.709, K.732, P.733, A.734, 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 Ligands: MG.13 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:P.707, B:F.944 Hydrogen bonds: B:S.706, B:N.709, B:K.732, B:G.784, B:S.785, B:S.785, B:E.812 Water bridges: B:E.735, B:E.735, B:N.896, B:F.944, B:F.944, B:F.944, B:F.944

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

SO4.3: 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 SO4.4: 3 residues within 4Å: Chain A: S.1196, G.1198, R.1202 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.1196 Water bridges: A:S.1196, A:G.1198, A:E.1199 Salt bridges: A:R.1202 SO4.5: 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:E.856, A:D.857, A:R.955 Water bridges: A:D.956 SO4.6: 2 residues within 4Å: Chain A: K.1062, K.1141 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.1062 SO4.15: 7 residues within 4Å: Chain A: R.690, P.1041, Q.1042 Chain B: S.96, Q.98, E.99, 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 SO4.16: 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:Q.98, 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

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

PGE.7: 8 residues within 4Å: Chain A: H.1047, L.1080, G.1081, L.1082, D.1083, T.1097, L.1098, H.1099 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.1083 PGE.17: 6 residues within 4Å: Chain B: H.1047, L.1080, G.1081, L.1082, L.1098, H.1099 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.1083 PGE.19: 2 residues within 4Å: Chain B: A.583, T.584 1 PLIP interactions: 1 interactions with chain B Water bridges: B:S.756

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

FMT.8: 3 residues within 4Å: Chain A: N.557, T.560 Ligands: FMT.11 No protein-ligand interaction detected (PLIP) FMT.9: 2 residues within 4Å: Chain A: A.409, M.436 No protein-ligand interaction detected (PLIP) FMT.10: 2 residues within 4Å: Chain A: Y.434, G.438 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.438 Water bridges: A:G.438 FMT.11: 5 residues within 4Å: Chain A: R.42, L.388, A.389, D.554 Ligands: FMT.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.389, A:N.557 Water bridges: A:D.554, A:T.560 FMT.20: 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:R.845, B:S.847, B:G.1004, B:A.1005 Water bridges: B:S.847, B:I.1003

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

MG.13: 1 residues within 4Å: Ligands: NAI.14 No protein-ligand interaction detected (PLIP)

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

PEG.18: 4 residues within 4Å: Chain B: G.544, D.545, T.548, R.689 No protein-ligand interaction detected (PLIP)

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Bifunctional protein PutA

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