SMTL ID : 8rkr.1

Structure of human DELTA-1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE (ALDH4A1) complexed with a monophosphate-tweezer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

homo-dimer

Ligands

1 x 01: (1R,5S,9S,16R,20R,24S,28S,35R)-22-(Dihydroxyphosphoryloxy)tridecacyclo[22.14.1.15,20.19,16.128,35.02,23.04,21.06,19.08,17.010,15.025,38.027,36.029,34]dotetraconta-2(23),3,6,8(17),10,12,14,18,21,25,27(36),29,31,33,37-pentadecaen-3-ol

01.1: 5 residues within 4Å: Chain A: R.403, K.406, W.407, E.409, H.410 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:K.406, A:K.406, A:K.406, A:W.407, A:W.407, A:W.407, A:H.410 Hydrogen bonds: A:E.409 Water bridges: A:K.406, A:K.406, A:K.406, A:K.406 Salt bridges: A:K.406 pi-Cation interactions: A:K.406, A:K.406, A:K.406, A:K.406, A:K.406

4 x BEZ: BENZOIC ACID(Non-covalent)

BEZ.2: 8 residues within 4Å: Chain A: E.169, F.216, I.219, S.353, T.515, G.516, S.517, F.524 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.219 Hydrogen bonds: A:S.353, A:G.516, A:S.517, A:S.517 pi-Stacking: A:F.216, A:F.524 BEZ.3: 4 residues within 4Å: Chain A: M.65, E.66, A.67, K.97 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.67, A:K.97 Salt bridges: A:K.97 BEZ.4: 8 residues within 4Å: Chain B: E.169, F.216, I.219, S.353, T.515, G.516, S.517, F.524 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.219 Hydrogen bonds: B:S.353, B:G.516, B:S.517 pi-Stacking: B:F.216, B:F.524 BEZ.5: 3 residues within 4Å: Chain B: M.65, E.66, A.67 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.67 Salt bridges: B:K.97

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Porfetye, A.T. et al., How Do Molecular Tweezers Bind to Proteins? Lessons from X-ray Crystallography. Molecules (2024)

Release Date

2024-05-08

Peptides

Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial

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