SMTL ID : 5cnx.1 (1 other biounit)

Crystal structure of Xaa-Pro aminopeptidase from Escherichia coli K12

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: D.223, H.292, T.319, E.321, E.335 Ligands: ZN.2, CAC.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.223, A:H.292, A:E.321, A:E.335 ZN.2: 8 residues within 4Å: Chain A: F.181, D.212, D.223, T.225, E.321, E.335 Ligands: ZN.1, CAC.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.212, A:D.212, A:D.223, A:E.335, A:E.335 ZN.6: 7 residues within 4Å: Chain B: D.223, H.292, T.319, E.321, E.335 Ligands: ZN.7, CAC.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.223, B:H.292, B:E.321, B:E.335 ZN.7: 8 residues within 4Å: Chain B: F.181, D.212, D.223, T.225, E.321, E.335 Ligands: ZN.6, CAC.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.212, B:D.212, B:D.223, B:E.335

2 x CAC: CACODYLATE ION(Non-covalent)

CAC.3: 12 residues within 4Å: Chain A: F.181, I.184, H.195, D.212, D.223, H.292, V.298, H.299, E.321, E.335 Ligands: ZN.1, ZN.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.223 CAC.8: 10 residues within 4Å: Chain B: I.184, D.212, D.223, H.292, V.298, H.299, E.321, E.335 Ligands: ZN.6, ZN.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.223

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: R.24, T.35, G.36, S.37, Y.55 Chain B: K.197 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.24, A:R.24, A:G.36, A:S.37, A:S.37, A:Y.55, B:K.197

1 x NA: SODIUM ION(Non-functional Binders)

NA.5: 3 residues within 4Å: Chain A: Q.109, L.112, A.114 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.109, A:A.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Are, V.N. et al., Structures and activities of widely conserved small prokaryotic aminopeptidases-P clarify classification of M24B peptidases. Proteins (2018)

Release Date

2016-07-20

Peptides

Aminopeptidase YpdF: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Aminopeptidase YpdF

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