SMTL ID : 3var.1

Crystal structure of DNPEP, ZnZn form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-12-mer

Ligands

24 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: H.115, D.285, N.286, E.322, E.323, D.367 Ligands: ZN.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.115, A:D.285, A:D.367, A:D.367, H2O.7 ZN.2: 4 residues within 4Å: Chain A: D.285, E.323, H.461 Ligands: ZN.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.285, A:E.323, A:E.323, A:H.461, H2O.7 ZN.3: 7 residues within 4Å: Chain B: H.115, D.285, N.286, E.322, E.323, D.367 Ligands: ZN.4 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.115, B:D.285, B:D.367, B:D.367, H2O.14 ZN.4: 4 residues within 4Å: Chain B: D.285, E.323, H.461 Ligands: ZN.3 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.285, B:E.323, B:E.323, B:H.461, H2O.14 ZN.5: 7 residues within 4Å: Chain C: H.115, D.285, N.286, E.322, E.323, D.367 Ligands: ZN.6 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.115, C:D.285, C:D.367, C:D.367, H2O.20 ZN.6: 4 residues within 4Å: Chain C: D.285, E.323, H.461 Ligands: ZN.5 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.285, C:E.323, C:E.323, C:H.461, H2O.20 ZN.7: 7 residues within 4Å: Chain D: H.115, D.285, N.286, E.322, E.323, D.367 Ligands: ZN.8 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.115, D:D.285, D:D.367, D:D.367, H2O.27 ZN.8: 4 residues within 4Å: Chain D: D.285, E.323, H.461 Ligands: ZN.7 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.285, D:E.323, D:E.323, D:H.461, H2O.27 ZN.9: 7 residues within 4Å: Chain E: H.115, D.285, N.286, E.322, E.323, D.367 Ligands: ZN.10 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.115, E:D.285, E:D.367, E:D.367, H2O.34 ZN.10: 4 residues within 4Å: Chain E: D.285, E.323, H.461 Ligands: ZN.9 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.285, E:E.323, E:E.323, E:H.461, H2O.34 ZN.11: 7 residues within 4Å: Chain F: H.115, D.285, N.286, E.322, E.323, D.367 Ligands: ZN.12 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.115, F:D.285, F:D.367, F:D.367, H2O.40 ZN.12: 4 residues within 4Å: Chain F: D.285, E.323, H.461 Ligands: ZN.11 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.285, F:E.323, F:E.323, F:H.461, H2O.40 ZN.13: 7 residues within 4Å: Chain G: H.115, D.285, N.286, E.322, E.323, D.367 Ligands: ZN.14 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:H.115, G:D.285, G:D.367, G:D.367, H2O.47 ZN.14: 4 residues within 4Å: Chain G: D.285, E.323, H.461 Ligands: ZN.13 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.285, G:E.323, G:E.323, G:H.461, H2O.47 ZN.15: 7 residues within 4Å: Chain H: H.115, D.285, N.286, E.322, E.323, D.367 Ligands: ZN.16 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:H.115, H:D.285, H:D.367, H:D.367, H2O.54 ZN.16: 4 residues within 4Å: Chain H: D.285, E.323, H.461 Ligands: ZN.15 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.285, H:E.323, H:E.323, H:H.461, H2O.54 ZN.17: 7 residues within 4Å: Chain I: H.115, D.285, N.286, E.322, E.323, D.367 Ligands: ZN.18 5 PLIP interactions: 4 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:H.115, I:D.285, I:D.367, I:D.367, H2O.60 ZN.18: 4 residues within 4Å: Chain I: D.285, E.323, H.461 Ligands: ZN.17 5 PLIP interactions: 4 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:D.285, I:E.323, I:E.323, I:H.461, H2O.60 ZN.19: 7 residues within 4Å: Chain J: H.115, D.285, N.286, E.322, E.323, D.367 Ligands: ZN.20 5 PLIP interactions: 4 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:H.115, J:D.285, J:D.367, J:D.367, H2O.67 ZN.20: 4 residues within 4Å: Chain J: D.285, E.323, H.461 Ligands: ZN.19 5 PLIP interactions: 4 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:D.285, J:E.323, J:E.323, J:H.461, H2O.67 ZN.21: 7 residues within 4Å: Chain K: H.115, D.285, N.286, E.322, E.323, D.367 Ligands: ZN.22 5 PLIP interactions: 4 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:H.115, K:D.285, K:D.367, K:D.367, H2O.74 ZN.22: 4 residues within 4Å: Chain K: D.285, E.323, H.461 Ligands: ZN.21 5 PLIP interactions: 4 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:D.285, K:E.323, K:E.323, K:H.461, H2O.74 ZN.23: 7 residues within 4Å: Chain L: H.115, D.285, N.286, E.322, E.323, D.367 Ligands: ZN.24 5 PLIP interactions: 4 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:H.115, L:D.285, L:D.367, L:D.367, H2O.80 ZN.24: 4 residues within 4Å: Chain L: D.285, E.323, H.461 Ligands: ZN.23 5 PLIP interactions: 4 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:D.285, L:E.323, L:E.323, L:H.461, H2O.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Y. et al., Insights into substrate specificity and metal activation of Mammalian tetrahedral aspartyl aminopeptidase. J.Biol.Chem. (2012)

Release Date

2012-02-29

Peptides

Aspartyl aminopeptidase: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

I
A

J
A

K
A

L
A

Aspartyl aminopeptidase

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