SMTL ID : 6x9a.2 (2 other biounits)

Structure of proline utilization A with trans-4-hydroxy-D-proline bound in the L-glutamate-gamma-semialdehyde dehydrogenase active site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.41 Å

Oligo State

monomer

Ligands

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

FAD.1: 32 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, L.451, Y.475, E.494, N.495, S.499, S.500, F.501, I.1234, G.1235 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:H.425, A:N.426, A:E.494, A:S.499, A:F.501, A:G.1235 Water bridges: A:E.494, 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 PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2: 4 residues within 4Å: Chain A: L.1080, G.1081, L.1098, H.1099 No protein-ligand interaction detected (PLIP)

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

PEG.3: 5 residues within 4Å: Chain A: G.544, D.545, R.547, T.548, R.689 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.544 Water bridges: A:T.548, A:R.689, A:R.689

1 x UY7: (4S)-4-hydroxy-D-proline(Non-covalent)

UY7.4: 9 residues within 4Å: Chain A: E.676, F.710, I.714, R.845, S.847, I.1003, G.1004, A.1005, F.1012 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.1012 Hydrogen bonds: A:S.847, A:G.1004, A:A.1005 Water bridges: A:E.676, A:S.847 Salt bridges: A:R.845

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

SO4.5: 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 SO4.6: 1 residues within 4Å: Chain A: R.204 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.204 Salt bridges: A:R.204 SO4.7: 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 SO4.8: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Campbell, A.C. et al., Structural analysis of prolines and hydroxyprolines binding to the l-glutamate-gamma-semialdehyde dehydrogenase active site of bifunctional proline utilization A. Arch.Biochem.Biophys. (2020)

Release Date

2020-12-30

Peptides

Bifunctional protein PutA: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Bifunctional protein PutA

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