SMTL ID : 4ou3.1

Crystal structure of porcine aminopeptidase N complexed with CNGRCG tumor-homing peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x CYS- ASN- GLY- ARG- CYS- GLY: tumor-homing peptide(Non-covalent)

CYS-ASN-GLY-ARG-CYS-GLY.1: 17 residues within 4Å: Chain A: Q.146, S.147, N.283, A.284, G.285, A.286, M.287, E.288, R.296, H.321, E.322, E.344, S.402, F.405, Y.410 Ligands: ZN.10, SO4.18 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:Q.146, A:S.147, A:N.283, A:A.284, A:A.286, A:A.286, A:R.296, A:R.296, A:S.402, A:Y.410 Water bridges: A:Q.144, A:Q.146, A:T.148, A:H.321, A:H.321, A:E.351 CYS-ASN-GLY-ARG-CYS-GLY.23: 17 residues within 4Å: Chain B: Q.146, S.147, N.283, A.284, G.285, A.286, M.287, E.288, R.296, H.321, E.322, E.344, S.402, F.405, Y.410 Ligands: ZN.32, SO4.40 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:S.147, B:N.283, B:A.284, B:A.286, B:A.286, B:E.288, B:R.296, B:R.296 Water bridges: B:Q.144, B:Q.146, B:T.148, B:H.321, B:E.344, B:E.351, B:E.351

16 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: N.20, I.42, E.110 Ligands: NAG-NAG.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.185 NAG-NAG.3: 5 residues within 4Å: Chain A: I.36, N.62, Q.116, G.117, E.118 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 8 residues within 4Å: Chain A: S.18, Y.19, N.20, R.44, N.167, T.204 Ligands: NAG-NAG.2, NAG-NAG.2 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.44 NAG-NAG.5: 3 residues within 4Å: Chain A: K.138, N.175, E.219 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: Y.249, N.252, F.302, K.312 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain A: N.266 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain A: L.15, A.161, F.440, Q.443, N.444 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.443 NAG-NAG.9: 4 residues within 4Å: Chain A: D.366, M.530, V.559, N.560 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain B: N.20, I.42, E.110 Ligands: NAG-NAG.26 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.185 NAG-NAG.25: 5 residues within 4Å: Chain B: I.36, N.62, Q.116, G.117, E.118 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 8 residues within 4Å: Chain B: S.18, Y.19, N.20, R.44, N.167, T.204 Ligands: NAG-NAG.24, NAG-NAG.24 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.44 NAG-NAG.27: 3 residues within 4Å: Chain B: K.138, N.175, E.219 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 4 residues within 4Å: Chain B: Y.249, N.252, F.302, K.312 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 1 residues within 4Å: Chain B: N.266 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 5 residues within 4Å: Chain B: L.15, A.161, F.440, Q.443, N.444 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Q.443 NAG-NAG.31: 4 residues within 4Å: Chain B: D.366, M.530, V.559, N.560 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.10: 4 residues within 4Å: Chain A: H.321, H.325, E.344 Ligands: CYS-ASN-GLY-ARG-CYS-GLY.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.321, A:H.325, A:E.344, A:E.344, H2O.6 ZN.32: 4 residues within 4Å: Chain B: H.321, H.325, E.344 Ligands: CYS-ASN-GLY-ARG-CYS-GLY.23 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.321, B:H.325, B:E.344, B:E.344, H2O.40

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

NAG.11: 2 residues within 4Å: Chain A: D.489, N.494 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.489, A:N.494 NAG.12: 2 residues within 4Å: Chain A: N.584, V.587 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.584 NAG.33: 2 residues within 4Å: Chain B: D.489, N.494 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.494 NAG.34: 2 residues within 4Å: Chain B: N.584, V.587 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.584

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

SO4.13: 5 residues within 4Å: Chain A: Y.349, L.353, K.365, R.418, N.422 Ligand excluded by PLIP SO4.14: 5 residues within 4Å: Chain A: G.740, Q.741, E.772 Chain B: K.654, R.658 Ligand excluded by PLIP SO4.15: 6 residues within 4Å: Chain A: P.280, D.281, R.296, E.297, N.298, V.757 Ligand excluded by PLIP SO4.16: 6 residues within 4Å: Chain A: T.22, R.24, K.38, G.39, K.40, I.171 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain A: P.256, N.259, H.357 Ligand excluded by PLIP SO4.18: 6 residues within 4Å: Chain A: F.405, D.406, S.407, Y.410 Ligands: CYS-ASN-GLY-ARG-CYS-GLY.1, SO4.20 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain A: Y.686, I.689, N.690 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain A: D.406, S.407 Ligands: SO4.18 Ligand excluded by PLIP SO4.21: 8 residues within 4Å: Chain A: P.160, Y.211, T.333, L.334, W.336, W.337, L.340, N.343 Ligand excluded by PLIP SO4.22: 5 residues within 4Å: Chain A: S.308, S.310, N.311, R.314, K.762 Ligand excluded by PLIP SO4.35: 5 residues within 4Å: Chain B: Y.349, L.353, K.365, R.418, N.422 Ligand excluded by PLIP SO4.36: 5 residues within 4Å: Chain A: K.654, R.658 Chain B: G.740, Q.741, E.772 Ligand excluded by PLIP SO4.37: 6 residues within 4Å: Chain B: P.280, D.281, R.296, E.297, N.298, V.757 Ligand excluded by PLIP SO4.38: 6 residues within 4Å: Chain B: T.22, R.24, K.38, G.39, K.40, I.171 Ligand excluded by PLIP SO4.39: 3 residues within 4Å: Chain B: P.256, N.259, H.357 Ligand excluded by PLIP SO4.40: 6 residues within 4Å: Chain B: F.405, D.406, S.407, Y.410 Ligands: CYS-ASN-GLY-ARG-CYS-GLY.23, SO4.42 Ligand excluded by PLIP SO4.41: 3 residues within 4Å: Chain B: Y.686, I.689, N.690 Ligand excluded by PLIP SO4.42: 3 residues within 4Å: Chain B: D.406, S.407 Ligands: SO4.40 Ligand excluded by PLIP SO4.43: 8 residues within 4Å: Chain B: P.160, Y.211, T.333, L.334, W.336, W.337, L.340, N.343 Ligand excluded by PLIP SO4.44: 5 residues within 4Å: Chain B: S.308, S.310, N.311, R.314, K.762 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, C. et al., A Unified Mechanism for Aminopeptidase N-based Tumor Cell Motility and Tumor-homing Therapy. J.Biol.Chem. (2014)

Release Date

2014-11-05

Peptides

Aminopeptidase N: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Aminopeptidase N

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