SMTL ID : 4dyo.2 (1 other biounit)

Crystal Structure of Human Aspartyl Aminopeptidase (DNPEP) in complex with Aspartic acid Hydroxamate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: D.274, E.312, H.450 Ligands: ZN.2, SD4.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.274, A:E.312, A:E.312, A:H.450 ZN.2: 8 residues within 4Å: Chain A: H.104, D.274, N.275, E.311, E.312, D.356 Ligands: ZN.1, SD4.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.104, A:D.274, A:D.356, A:D.356 ZN.11: 5 residues within 4Å: Chain B: D.274, E.312, H.450 Ligands: ZN.12, SD4.14 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.274, B:E.312, B:E.312, B:H.450 ZN.12: 8 residues within 4Å: Chain B: H.104, D.274, N.275, E.311, E.312, D.356 Ligands: ZN.11, SD4.14 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.104, B:D.274, B:D.356, B:D.356

2 x MG: MAGNESIUM ION(Non-functional Binders)

MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x SD4: N-hydroxy-L-asparagine(Non-covalent)

SD4.4: 16 residues within 4Å: Chain A: H.104, D.274, E.311, E.312, D.356, M.357, H.359, K.384, Y.391, G.424, T.425, M.449, H.450 Chain B: H.180 Ligands: ZN.1, ZN.2 8 PLIP interactions: 1 interactions with chain B, 7 interactions with chain A Salt bridges: B:H.180, A:H.359, A:K.384 Hydrogen bonds: A:M.357, A:K.384, A:Y.391, A:G.424, A:T.425 SD4.14: 16 residues within 4Å: Chain A: H.180 Chain B: H.104, D.274, E.311, E.312, D.356, M.357, H.359, K.384, Y.391, G.424, T.425, M.449, H.450 Ligands: ZN.11, ZN.12 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:M.357, B:K.384, B:G.424, B:T.425 Water bridges: B:Y.391, B:Y.391 Salt bridges: B:H.359, B:K.384, A:H.180

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: T.77, R.78, N.79, S.80 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.77, A:T.77, A:N.79, A:S.80 Water bridges: A:E.62, A:T.77 GOL.6: 5 residues within 4Å: Chain A: P.363, N.364, Y.365, L.366, D.367 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:L.366, A:D.367, A:D.367 Water bridges: B:Q.120 GOL.7: 6 residues within 4Å: Chain A: N.372, H.373, R.374, P.375, Q.413, D.414 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.372, A:R.374, A:R.374, A:D.414, A:D.414, A:D.414 GOL.8: 5 residues within 4Å: Chain A: I.179, H.180, R.183 Chain B: G.133, H.450 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.180, A:R.183, B:G.133 Water bridges: A:R.183 GOL.9: 2 residues within 4Å: Chain A: Q.322, R.434 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.322 Water bridges: A:R.434 GOL.10: 5 residues within 4Å: Chain A: D.367, K.368, R.418, D.420, T.421 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.367 GOL.15: 4 residues within 4Å: Chain B: T.77, R.78, N.79, S.80 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.77, B:N.79, B:S.80 Water bridges: B:E.62, B:T.77, B:T.77 GOL.16: 5 residues within 4Å: Chain B: P.363, N.364, Y.365, L.366, D.367 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.366, B:D.367, B:D.367 Water bridges: A:Q.120 GOL.17: 6 residues within 4Å: Chain B: N.372, H.373, R.374, P.375, Q.413, D.414 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.372, B:R.374, B:R.374, B:D.414, B:D.414 GOL.18: 5 residues within 4Å: Chain A: G.133, H.450 Chain B: I.179, H.180, R.183 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.133, B:H.180, B:R.183 Water bridges: B:R.183 GOL.19: 2 residues within 4Å: Chain B: Q.322, R.434 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.322 Water bridges: B:R.434 GOL.20: 5 residues within 4Å: Chain B: D.367, K.368, R.418, D.420, T.421 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.367

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chaikuad, A. et al., Structure of human aspartyl aminopeptidase complexed with substrate analogue: insight into catalytic mechanism, substrate specificity and M18 peptidase family. Bmc Struct.Biol. (2012)

Release Date

2012-03-14

Peptides

Aspartyl aminopeptidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Aspartyl aminopeptidase

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