SMTL ID : 4fys.1

Human aminopeptidase N (CD13) in complex with angiotensin IV

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

monomer

Ligands

1 x VAL- TYR- ILE- HIS- PRO- PHE: Angiotensin IV(Non-covalent)

VAL-TYR-ILE-HIS-PRO-PHE.1: 21 residues within 4Å: Chain A: Q.147, Q.149, A.287, G.288, A.289, M.290, E.291, R.317, V.321, H.324, E.325, E.347, E.354, R.378, F.408, Y.413, F.832, S.833, N.836, Q.839, R.843 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:A.287, A:V.321, A:H.324, A:F.408, A:F.408, A:F.832, A:F.832 Hydrogen bonds: A:Q.149, A:G.288, A:A.289, A:A.289, A:R.317, A:R.378, A:Y.413 Water bridges: A:E.347, A:R.378, A:Q.839 Salt bridges: A:R.378 pi-Stacking: A:H.324

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.2: 7 residues within 4Å: Chain A: S.20, Y.21, R.22, T.44, R.46, N.170, T.207 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.46, A:R.46

1 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: 5 residues within 4Å: Chain A: N.366, D.369, Q.532, L.560, N.561 No protein-ligand interaction detected (PLIP)

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

NAG.4: 5 residues within 4Å: Chain A: V.38, N.64, E.119, G.120, E.121 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.38 Hydrogen bonds: A:N.64 Water bridges: A:E.119 NAG.5: 6 residues within 4Å: Chain A: H.175, K.177, L.179, S.191, P.193, N.201 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.177, A:S.191, A:N.201 Water bridges: A:T.203 NAG.6: 2 residues within 4Å: Chain A: Y.252, N.255 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.252 Hydrogen bonds: A:N.255 NAG.7: 4 residues within 4Å: Chain A: P.611, T.613, L.614, N.617 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.611, A:L.614 Hydrogen bonds: A:T.613, A:T.613, A:N.617 NAG.8: 5 residues within 4Å: Chain A: Q.434, S.438, E.459, A.460, N.463 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.459 Hydrogen bonds: A:Q.434, A:E.459, A:N.463

11 x SO4: SULFATE ION(Non-functional Binders)

SO4.9: 6 residues within 4Å: Chain A: L.67, G.70, H.71, R.72, K.88, T.89 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.70, A:R.72, A:T.89, A:T.89 Water bridges: A:R.72, A:R.72 Salt bridges: A:H.71 SO4.10: 4 residues within 4Å: Chain A: R.72, T.89, E.90, L.91 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.91 Water bridges: A:T.89 Salt bridges: A:R.72 SO4.11: 1 residues within 4Å: Chain A: R.626 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.626, A:R.626 Salt bridges: A:R.626 SO4.12: 4 residues within 4Å: Chain A: Y.134, M.135, R.241, R.791 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.135 Water bridges: A:R.791 Salt bridges: A:R.241, A:R.791 SO4.13: 2 residues within 4Å: Chain A: S.498, R.542 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.498 Salt bridges: A:R.542 SO4.14: 5 residues within 4Å: Chain A: S.311, S.313, N.314, S.730, K.763 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.311, A:S.313, A:S.313, A:N.314, A:S.730, A:S.730 Water bridges: A:S.730 Salt bridges: A:K.763 SO4.15: 1 residues within 4Å: Chain A: R.542 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.542 Salt bridges: A:R.542 SO4.16: 4 residues within 4Å: Chain A: N.64, Y.65, R.72, L.91 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.65 Water bridges: A:L.63, A:N.64 Salt bridges: A:R.72 SO4.17: 3 residues within 4Å: Chain A: N.672, P.680, E.681 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.672, A:E.681 Water bridges: A:N.672, A:N.682, A:N.682 SO4.18: 4 residues within 4Å: Chain A: H.586, S.587, R.594, Q.627 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.627 Salt bridges: A:R.594 SO4.19: 3 residues within 4Å: Chain A: T.899, E.900, K.903 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.899 Salt bridges: A:K.903

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wong, A.H. et al., The X-ray Crystal Structure of Human Aminopeptidase N Reveals a Novel Dimer and the Basis for Peptide Processing. J.Biol.Chem. (2012)

Release Date

2012-09-05

Peptides

Aminopeptidase N: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Aminopeptidase N

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