SMTL ID : 5ib9.1

Crystal structure of aminopeptidase equipped with PAD from Aneurinibacillus sp. AM-1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: D.240, E.273, Y.370, H.371 Ligands: ZN.2, BES.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.240, A:E.273, A:E.273, A:H.371 ZN.2: 8 residues within 4Å: Chain A: H.228, D.240, D.241, E.272, E.273, D.301 Ligands: ZN.1, BES.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.228, A:D.240, A:D.301, A:D.301 ZN.3: 4 residues within 4Å: Chain A: T.13, D.386, D.390 Ligands: ZN.4 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.386, A:D.390, H2O.7, H2O.11, H2O.16 ZN.4: 4 residues within 4Å: Chain A: T.10, T.13, D.386 Ligands: ZN.3 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.13, A:T.13, A:D.386, H2O.6, H2O.7, H2O.9 ZN.5: 1 residues within 4Å: Chain A: E.383 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.383, A:E.383, H2O.11 ZN.6: 2 residues within 4Å: Chain A: H.204 Chain B: E.288 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:H.204, B:E.288, H2O.15, H2O.16, H2O.37 ZN.8: 6 residues within 4Å: Chain B: D.240, E.273, Y.370, H.371 Ligands: ZN.9, BES.14 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.240, B:E.273, B:E.273, B:H.371 ZN.9: 8 residues within 4Å: Chain B: H.228, D.240, D.241, E.272, E.273, D.301 Ligands: ZN.8, BES.14 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.228, B:D.240, B:D.301, B:D.301 ZN.10: 4 residues within 4Å: Chain B: T.13, D.386, D.390 Ligands: ZN.11 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.386, B:D.390, H2O.29, H2O.34, H2O.38 ZN.11: 4 residues within 4Å: Chain B: T.10, T.13, D.386 Ligands: ZN.10 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.13, B:T.13, B:D.386, H2O.28, H2O.29, H2O.32 ZN.12: 1 residues within 4Å: Chain B: E.383 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.383, B:E.383, H2O.34 ZN.13: 2 residues within 4Å: Chain A: E.288 Chain B: H.204 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:H.204, A:E.288, H2O.15, H2O.38, H2O.38

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

BES.7: 15 residues within 4Å: Chain A: H.228, D.240, E.272, E.273, G.275, L.276, D.301, M.302, R.345, I.362, V.366, Y.370, H.371 Ligands: ZN.1, ZN.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.276, A:R.345, A:I.362, A:V.366, A:Y.370 Hydrogen bonds: A:D.240, A:R.345, A:Y.370 Salt bridges: A:R.345, A:H.371 pi-Cation interactions: A:R.345 BES.14: 15 residues within 4Å: Chain B: H.228, D.240, E.272, E.273, G.275, L.276, D.301, M.302, R.345, I.362, V.366, Y.370, H.371 Ligands: ZN.8, ZN.9 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.276, B:R.345, B:I.362, B:V.366, B:Y.370 Hydrogen bonds: B:D.240, B:R.345, B:Y.370 Salt bridges: B:R.345, B:H.371 pi-Cation interactions: B:R.345

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tagawa, R. et al., Crystal structure of aminopeptidase. To Be Published

Release Date

2017-02-22

Peptides

Aminopeptidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Aminopeptidase

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