SMTL ID : 4fyt.1

Human aminopeptidase N (CD13) in complex with amastatin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x L2O- VAL- VAL- ASP: AMASTATIN(Non-covalent)

L2O-VAL-VAL-ASP.1: 18 residues within 4Å: Chain A: Q.147, Q.149, A.287, G.288, A.289, M.290, E.291, R.299, N.301, R.317, H.324, E.325, H.328, E.347, F.408, Y.413, F.832 Ligands: ZN.10 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.408, A:F.408, A:F.832, A:F.832 Hydrogen bonds: A:Q.149, A:Q.149, A:G.288, A:A.289, A:A.289, A:E.291, A:Y.413 Water bridges: A:E.347, A:N.836 Salt bridges: A:R.299, A:R.299, A:R.317 L2O-VAL-VAL-ASP.23: 18 residues within 4Å: Chain B: Q.147, Q.149, A.287, G.288, A.289, M.290, E.291, R.299, N.301, R.317, H.324, E.325, H.328, E.347, F.408, Y.413, F.832 Ligands: ZN.32 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:F.408, B:F.408, B:F.832, B:F.832 Hydrogen bonds: B:Q.149, B:Q.149, B:G.288, B:A.289, B:A.289, B:E.291, B:Y.413 Water bridges: B:E.347, B:N.836 Salt bridges: B:R.299, B:R.299, B:R.317

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

NAG-NAG.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 NAG-NAG.3: 4 residues within 4Å: Chain A: D.369, Q.532, L.560, N.561 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: P.611, T.613, L.614, N.617 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 7 residues within 4Å: Chain B: S.20, Y.21, R.22, T.44, R.46, N.170, T.207 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.46, B:R.46 NAG-NAG.25: 4 residues within 4Å: Chain B: D.369, Q.532, L.560, N.561 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 4 residues within 4Å: Chain B: P.611, T.613, L.614, N.617 No protein-ligand interaction detected (PLIP)

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

NAG.5: 5 residues within 4Å: Chain A: V.38, N.64, E.119, G.120, E.121 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.38 Hydrogen bonds: A:N.64 NAG.6: 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.7: 3 residues within 4Å: Chain A: Y.252, N.255, P.307 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.252, A:P.307 Hydrogen bonds: A:N.255, A:K.315 NAG.8: 5 residues within 4Å: Chain A: Q.434, S.438, E.459, A.460, N.463 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.459 Hydrogen bonds: A:Q.434, A:E.459, A:E.459, A:N.463 NAG.9: 2 residues within 4Å: Chain A: N.720, N.754 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.720, A:N.754 NAG.27: 5 residues within 4Å: Chain B: V.38, N.64, E.119, G.120, E.121 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.38 Hydrogen bonds: B:N.64 NAG.28: 6 residues within 4Å: Chain B: H.175, K.177, L.179, S.191, P.193, N.201 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.177, B:S.191, B:N.201 Water bridges: B:T.203 NAG.29: 3 residues within 4Å: Chain B: Y.252, N.255, P.307 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.252, B:P.307 Hydrogen bonds: B:N.255, B:K.315 NAG.30: 5 residues within 4Å: Chain B: Q.434, S.438, E.459, A.460, N.463 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:E.459 Hydrogen bonds: B:Q.434, B:E.459, B:E.459, B:N.463 NAG.31: 2 residues within 4Å: Chain B: N.720, N.754 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.720, B:N.754

2 x ZN: ZINC ION(Non-covalent)

ZN.10: 4 residues within 4Å: Chain A: H.324, H.328, E.347 Ligands: L2O-VAL-VAL-ASP.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.324, A:H.328, A:E.347 ZN.32: 4 residues within 4Å: Chain B: H.324, H.328, E.347 Ligands: L2O-VAL-VAL-ASP.23 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.324, B:H.328, B:E.347

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

SO4.11: 6 residues within 4Å: Chain A: L.67, G.70, H.71, R.72, K.88, T.89 Ligand excluded by PLIP SO4.12: 4 residues within 4Å: Chain A: R.72, T.89, E.90, L.91 Ligand excluded by PLIP SO4.13: 1 residues within 4Å: Chain A: R.626 Ligand excluded by PLIP SO4.14: 2 residues within 4Å: Chain A: S.498, R.542 Ligand excluded by PLIP SO4.15: 5 residues within 4Å: Chain A: S.311, S.313, N.314, S.730, K.763 Ligand excluded by PLIP SO4.16: 1 residues within 4Å: Chain A: R.542 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain A: N.64, Y.65, R.72, L.91 Ligand excluded by PLIP SO4.18: 5 residues within 4Å: Chain A: Y.651, K.655, V.806 Chain B: E.773, W.775 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain A: N.672, P.680, E.681 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain A: T.899, E.900, K.903 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain A: H.586, S.587, R.594, Q.627 Ligand excluded by PLIP SO4.22: 4 residues within 4Å: Chain A: Y.134, M.135, R.241, R.791 Ligand excluded by PLIP SO4.33: 6 residues within 4Å: Chain B: L.67, G.70, H.71, R.72, K.88, T.89 Ligand excluded by PLIP SO4.34: 4 residues within 4Å: Chain B: R.72, T.89, E.90, L.91 Ligand excluded by PLIP SO4.35: 1 residues within 4Å: Chain B: R.626 Ligand excluded by PLIP SO4.36: 2 residues within 4Å: Chain B: S.498, R.542 Ligand excluded by PLIP SO4.37: 5 residues within 4Å: Chain B: S.311, S.313, N.314, S.730, K.763 Ligand excluded by PLIP SO4.38: 1 residues within 4Å: Chain B: R.542 Ligand excluded by PLIP SO4.39: 4 residues within 4Å: Chain B: N.64, Y.65, R.72, L.91 Ligand excluded by PLIP SO4.40: 5 residues within 4Å: Chain A: E.773, W.775 Chain B: Y.651, K.655, V.806 Ligand excluded by PLIP SO4.41: 3 residues within 4Å: Chain B: N.672, P.680, E.681 Ligand excluded by PLIP SO4.42: 3 residues within 4Å: Chain B: T.899, E.900, K.903 Ligand excluded by PLIP SO4.43: 4 residues within 4Å: Chain B: H.586, S.587, R.594, Q.627 Ligand excluded by PLIP SO4.44: 4 residues within 4Å: Chain B: Y.134, M.135, R.241, R.791 Ligand excluded by PLIP

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Aminopeptidase N

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