SMTL ID : 3vat.1

Crystal structure of DNPEP, ZnMg form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-12-mer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.285, E.323, H.461 Ligands: MG.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.285, A:E.323, A:H.461, H2O.1, H2O.4 ZN.3: 4 residues within 4Å: Chain B: D.285, E.323, H.461 Ligands: MG.4 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.285, B:E.323, B:H.461, H2O.11, H2O.15 ZN.5: 4 residues within 4Å: Chain C: D.285, E.323, H.461 Ligands: MG.6 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.285, C:E.323, C:H.461, H2O.21, H2O.25 ZN.7: 4 residues within 4Å: Chain D: D.285, E.323, H.461 Ligands: MG.8 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.285, D:E.323, D:H.461, H2O.32, H2O.35 ZN.9: 4 residues within 4Å: Chain E: D.285, E.323, H.461 Ligands: MG.10 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.285, E:E.323, E:H.461, H2O.42, H2O.45 ZN.11: 4 residues within 4Å: Chain F: D.285, E.323, H.461 Ligands: MG.12 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.285, F:E.323, F:H.461, H2O.52, H2O.56 ZN.13: 4 residues within 4Å: Chain G: D.285, E.323, H.461 Ligands: MG.14 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.285, G:E.323, G:H.461, H2O.62, H2O.66 ZN.15: 4 residues within 4Å: Chain H: D.285, E.323, H.461 Ligands: MG.16 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:D.285, H:E.323, H:H.461, H2O.73, H2O.76 ZN.17: 4 residues within 4Å: Chain I: D.285, E.323, H.461 Ligands: MG.18 5 PLIP interactions: 3 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:D.285, I:E.323, I:H.461, H2O.83, H2O.86 ZN.19: 4 residues within 4Å: Chain J: D.285, E.323, H.461 Ligands: MG.20 5 PLIP interactions: 3 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:D.285, J:E.323, J:H.461, H2O.93, H2O.97 ZN.21: 4 residues within 4Å: Chain K: D.285, E.323, H.461 Ligands: MG.22 5 PLIP interactions: 3 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:D.285, K:E.323, K:H.461, H2O.103, H2O.107 ZN.23: 4 residues within 4Å: Chain L: D.285, E.323, H.461 Ligands: MG.24 5 PLIP interactions: 3 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:D.285, L:E.323, L:H.461, H2O.114, H2O.117

12 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: H.115, D.285, E.322, E.323, D.367 Ligands: ZN.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.115, A:D.285, A:D.367, H2O.1, H2O.4 MG.4: 6 residues within 4Å: Chain B: H.115, D.285, E.322, E.323, D.367 Ligands: ZN.3 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.115, B:D.285, B:D.367, H2O.11, H2O.15 MG.6: 6 residues within 4Å: Chain C: H.115, D.285, E.322, E.323, D.367 Ligands: ZN.5 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.115, C:D.285, C:D.367, H2O.21, H2O.25 MG.8: 6 residues within 4Å: Chain D: H.115, D.285, E.322, E.323, D.367 Ligands: ZN.7 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.115, D:D.285, D:D.367, H2O.32, H2O.35 MG.10: 6 residues within 4Å: Chain E: H.115, D.285, E.322, E.323, D.367 Ligands: ZN.9 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:H.115, E:D.285, E:D.367, H2O.42, H2O.45 MG.12: 6 residues within 4Å: Chain F: H.115, D.285, E.322, E.323, D.367 Ligands: ZN.11 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:H.115, F:D.285, F:D.367, H2O.52, H2O.56 MG.14: 6 residues within 4Å: Chain G: H.115, D.285, E.322, E.323, D.367 Ligands: ZN.13 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:H.115, G:D.285, G:D.367, H2O.62, H2O.66 MG.16: 6 residues within 4Å: Chain H: H.115, D.285, E.322, E.323, D.367 Ligands: ZN.15 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:H.115, H:D.285, H:D.367, H2O.73, H2O.76 MG.18: 6 residues within 4Å: Chain I: H.115, D.285, E.322, E.323, D.367 Ligands: ZN.17 5 PLIP interactions: 3 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:H.115, I:D.285, I:D.367, H2O.83, H2O.86 MG.20: 6 residues within 4Å: Chain J: H.115, D.285, E.322, E.323, D.367 Ligands: ZN.19 5 PLIP interactions: 3 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:H.115, J:D.285, J:D.367, H2O.93, H2O.97 MG.22: 6 residues within 4Å: Chain K: H.115, D.285, E.322, E.323, D.367 Ligands: ZN.21 5 PLIP interactions: 3 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:H.115, K:D.285, K:D.367, H2O.104, H2O.107 MG.24: 6 residues within 4Å: Chain L: H.115, D.285, E.322, E.323, D.367 Ligands: ZN.23 5 PLIP interactions: 3 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:H.115, L:D.285, L:D.367, H2O.114, H2O.117

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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