SMTL ID : 6x9c.2 (2 other biounits)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.44 Å

Oligo State

monomer

Ligands

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

NAI.1: 24 residues within 4Å: Chain A: I.705, S.706, P.707, W.708, N.709, K.732, A.734, E.735, D.764, G.765, G.768, A.769, F.782, G.784, S.785, V.788, I.792, E.812, T.813, G.814, C.846, E.942, F.944 Ligands: MG.6 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:P.707, A:F.944 Hydrogen bonds: A:S.706, A:S.706, A:N.709, A:K.732, A:E.735, A:G.784, A:S.785, A:E.812 Water bridges: A:S.785, A:C.846, A:N.896

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 FDA: DIHYDROFLAVINE-ADENINE DINUCLEOTIDE(Non-covalent)

FDA.3: 30 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 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:A.423, A:Q.449, A:Y.475, 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:S.499, A:F.501 Water bridges: A:K.397, A:A.423, 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

2 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: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

MG.6: 1 residues within 4Å: Ligands: NAI.1 No protein-ligand interaction detected (PLIP)

1 x PRO: PROLINE(Non-covalent)

PRO.7: 10 residues within 4Å: Chain A: E.676, F.710, I.714, R.845, C.846, S.847, I.1003, G.1004, A.1005, F.1012 9 PLIP interactions: 7 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:F.710, A:I.714, A:F.1012 Hydrogen bonds: A:S.847, A:G.1004, A:A.1005, P.7, P.7 Salt bridges: A:R.845

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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