SMTL ID : 4fyr.1

Human aminopeptidase N (CD13) in complex with bestatin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-dimer

Ligands

2 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: 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-BMA.23: 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

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.2: 4 residues within 4Å: Chain A: D.369, Q.532, L.560, N.561 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain B: D.369, Q.532, L.560, N.561 No protein-ligand interaction detected (PLIP)

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

NAG.3: 6 residues within 4Å: Chain A: L.36, V.38, N.64, E.119, G.120, E.121 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.38, A:E.119 Hydrogen bonds: A:N.64 Water bridges: A:E.119 NAG.4: 6 residues within 4Å: Chain A: H.175, K.177, L.179, S.191, P.193, N.201 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.191, A:N.201 Water bridges: A:T.203 NAG.5: 4 residues within 4Å: Chain A: Y.252, N.255, F.305, K.315 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.252, A:F.305 Hydrogen bonds: A:N.255, A:K.315 NAG.6: 4 residues within 4Å: Chain A: P.611, T.613, L.614, N.617 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.611, A:L.614 Hydrogen bonds: A:T.613, A:T.613 Water bridges: A:T.613, A:N.617, A:N.617 NAG.7: 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 NAG.8: 3 residues within 4Å: Chain A: N.720, N.754, T.756 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.720, A:N.720, A:N.754 NAG.9: 2 residues within 4Å: Chain A: N.671, N.674 No protein-ligand interaction detected (PLIP) NAG.25: 6 residues within 4Å: Chain B: L.36, V.38, N.64, E.119, G.120, E.121 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.38, B:E.119 Hydrogen bonds: B:N.64 Water bridges: B:E.119 NAG.26: 6 residues within 4Å: Chain B: H.175, K.177, L.179, S.191, P.193, N.201 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.191, B:N.201 Water bridges: B:T.203 NAG.27: 4 residues within 4Å: Chain B: Y.252, N.255, F.305, K.315 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.252, B:F.305 Hydrogen bonds: B:N.255, B:K.315 NAG.28: 4 residues within 4Å: Chain B: P.611, T.613, L.614, N.617 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:P.611, B:L.614 Hydrogen bonds: B:T.613, B:T.613 Water bridges: B:T.613, B:N.617, B:N.617 NAG.29: 5 residues within 4Å: Chain B: Q.434, S.438, E.459, A.460, N.463 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:E.459 Hydrogen bonds: B:Q.434, B:E.459, B:N.463 NAG.30: 3 residues within 4Å: Chain B: N.720, N.754, T.756 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.720, B:N.720, B:N.754 NAG.31: 2 residues within 4Å: Chain B: N.671, N.674 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.10: 5 residues within 4Å: Chain A: H.324, H.328, E.347, Y.413 Ligands: BES.11 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.324, A:H.328, A:E.347, A:E.347 ZN.32: 5 residues within 4Å: Chain B: H.324, H.328, E.347, Y.413 Ligands: BES.33 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.324, B:H.328, B:E.347, B:E.347

2 x BES: 2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID(Non-covalent)

BES.11: 16 residues within 4Å: Chain A: Q.149, A.150, A.287, A.289, E.291, V.321, H.324, E.325, H.328, E.347, S.405, F.408, Y.413, G.830, S.831 Ligands: ZN.10 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.321, A:F.408, A:F.408, A:Y.413 Hydrogen bonds: A:Q.147, A:Y.413 Water bridges: A:G.288 Salt bridges: A:H.324, A:H.328 BES.33: 16 residues within 4Å: Chain B: Q.149, A.150, A.287, A.289, E.291, V.321, H.324, E.325, H.328, E.347, S.405, F.408, Y.413, G.830, S.831 Ligands: ZN.32 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.321, B:F.408, B:F.408, B:Y.413 Hydrogen bonds: B:Q.147, B:Y.413 Water bridges: B:G.288 Salt bridges: B:H.324, B:H.328

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

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

2 x ACY: ACETIC ACID(Non-functional Binders)

ACY.22: 1 residues within 4Å: Chain A: R.473 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.473 Salt bridges: A:R.473 ACY.44: 1 residues within 4Å: Chain B: R.473 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.473 Salt bridges: B:R.473

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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