SMTL ID : 9csd.1

The Ectodomains of SPRING and S1P with the inhibitor PF-429242

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.40 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 13 residues within 4Å: Chain A: W.323, M.353, W.378, E.379, G.383, Y.384, R.386, V.513, N.515, S.550, S.552, Y.561, A.563 No protein-ligand interaction detected (PLIP)

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.2: 7 residues within 4Å: Chain A: N.728, T.729, S.730, D.771, G.772, G.811, L.815 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.728, A:T.729, A:S.730, A:D.771, A:D.771

1 x 01: 4-[(diethylamino)methyl]-N-[2-(2-methoxyphenyl)ethyl]-N-[(3R)-pyrrolidin-3-yl]benzamide

01.3: 26 residues within 4Å: Chain A: F.278, Q.282, V.283, S.284, Y.285, T.286, F.289, L.306, I.308, G.309, G.310, P.311, D.312, F.313, D.315, F.318, V.319, N.348, P.349, Y.633, P.649, L.650, F.737, D.739, N.741, W.746 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.278, A:I.308, A:D.312, A:D.315, A:F.318 Hydrogen bonds: A:D.312, A:D.312

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain A: N.630, L.631, D.655, D.697, E.699 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.655, A:D.697, A:E.699, A:E.699

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bullington, A.V. et al., Structural basis for substrate selectivity by site-one protease revealed by studies with a small-molecule inhibitor. Proc.Natl.Acad.Sci.USA (2025)

Release Date

2025-04-23

Peptides

Membrane-bound transcription factor site-1 protease: A
SREBP regulating gene protein: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane-bound transcription factor site-1 protease

SREBP regulating gene protein

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