SMTL ID : 8zi4.1

Cryo-EM structure of wtEP-trypsinogen

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

6 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: 1 residues within 4Å: Chain B: N.103 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 2 residues within 4Å: Chain B: N.125, Y.175 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 4 residues within 4Å: Chain C: T.317, Y.318, I.320, N.322 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 4 residues within 4Å: Chain C: H.386, Q.388, N.449, T.451 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 4 residues within 4Å: Chain C: N.544, Q.585, N.587 Ligands: NAG-NAG.4 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.544 NAG-NAG-BMA.12: 4 residues within 4Å: Chain C: L.82, N.154, S.156, E.157 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 3 residues within 4Å: Chain B: R.88, Q.158, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: N.196, N.197 Ligands: NAG-NAG-BMA.11 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.5: 1 residues within 4Å: Chain C: N.353 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.8: 4 residues within 4Å: Chain C: P.239, L.288, N.289, T.291 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.289

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.6: 3 residues within 4Å: Chain C: F.205, N.207, S.209 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.205

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.7: 4 residues within 4Å: Chain C: N.259, E.267, K.268, T.269 No protein-ligand interaction detected (PLIP)

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.13: 6 residues within 4Å: Chain B: E.9, H.60, M.61, N.64, T.66, Q.69 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.64, B:T.66 NAG.14: 5 residues within 4Å: Chain C: E.524, N.525, K.559, L.560, N.561 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.524, C:N.525, C:N.561 NAG.15: 7 residues within 4Å: Chain C: F.500, N.501, L.509, V.510, T.520, D.553, L.581 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.500, C:L.509 Hydrogen bonds: C:N.501, C:D.553, C:D.553 NAG.16: 9 residues within 4Å: Chain C: S.87, F.88, D.89, D.90, F.91, Y.143, N.147, A.148, T.149 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.88 Hydrogen bonds: C:D.89, C:D.89, C:D.90, C:N.147

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Song, Q.Y. et al., Structure of trypsinogen-engaged EP at 2.95 angstroms resolution. To Be Published

Release Date

2025-05-21

Peptides

Serine protease 1: A
Enteropeptidase catalytic light chain: B
Enteropeptidase non-catalytic heavy chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
A

Serine protease 1

Enteropeptidase catalytic light chain

Enteropeptidase non-catalytic heavy chain

Related Entries With Identical Sequence