SMTL ID : 9cam.1

Aminopeptidase N close state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

4 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: 8 residues within 4Å: Chain A: S.84, Y.85, R.86, T.108, R.110, N.234, K.252, T.271 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 2 residues within 4Å: Chain A: Y.316, N.319 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 5 residues within 4Å: Chain A: N.430, D.433, L.624, N.625, I.656 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.430 NAG-NAG-BMA.7: 7 residues within 4Å: Chain B: S.84, Y.85, R.86, T.108, R.110, N.234, T.271 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.4: 5 residues within 4Å: Chain A: K.241, S.255, T.256, P.257, N.265 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain B: Y.316, N.319 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain B: D.433, Q.596, L.624, N.625, I.656 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 6 residues within 4Å: Chain B: H.239, K.241, L.243, S.255, P.257, N.265 No protein-ligand interaction detected (PLIP)

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

NAG.9: 5 residues within 4Å: Chain A: R.98, V.102, N.128, G.184, E.185 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.102, A:E.185 Hydrogen bonds: A:R.98, A:N.128 NAG.11: 1 residues within 4Å: Chain A: N.527 No protein-ligand interaction detected (PLIP) NAG.12: 3 residues within 4Å: Chain A: T.677, L.678, N.681 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.678 Hydrogen bonds: A:T.677, A:T.677 NAG.13: 6 residues within 4Å: Chain B: L.100, V.102, N.128, E.183, G.184, E.185 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.102 NAG.15: 1 residues within 4Å: Chain B: N.527 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.527 NAG.16: 4 residues within 4Å: Chain B: E.636, T.677, L.678, N.681 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.678 Hydrogen bonds: B:N.681 NAG.17: 2 residues within 4Å: Chain B: E.814, N.818 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.818

2 x ZN: ZINC ION(Non-covalent)

ZN.10: 5 residues within 4Å: Chain A: E.355, H.388, H.392, E.411, Y.477 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.388, A:H.392, A:E.411 ZN.14: 5 residues within 4Å: Chain B: E.355, H.388, E.389, H.392, E.411 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.355, B:E.411

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lyu, M. et al., Aminopeptidase N close state. To Be Published

Release Date

2025-08-06

Peptides

Aminopeptidase N: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Aminopeptidase N

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