SMTL ID : 1lyb.1 (2 other biounits)

CRYSTAL STRUCTURES OF NATIVE AND INHIBITED FORMS OF HUMAN CATHEPSIN D: IMPLICATIONS FOR LYSOSOMAL TARGETING AND DRUG DESIGN

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-2-mer

Ligands

2 x IVA- VAL- VAL- STA- ALA- STA: PEPSTATIN(Non-covalent)

IVA-VAL-VAL-STA-ALA-STA.1: 16 residues within 4Å: Chain A: V.31, D.33, G.35, S.36, H.77, Y.78, G.79, S.80 Chain B: Y.100, D.126, G.128, T.129, S.130, E.155, I.206, I.215 15 PLIP interactions: 8 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:Y.100, B:T.129, B:I.206, A:V.31 Hydrogen bonds: B:G.128, B:T.129, B:T.129, B:S.130, B:S.130, A:G.35, A:H.77, A:G.79, A:S.80, A:S.80, A:S.80 IVA-VAL-VAL-STA-ALA-STA.4: 17 residues within 4Å: Chain C: D.33, G.35, S.36, H.77, Y.78, G.79, S.80 Chain D: F.26, I.29, Y.100, D.126, G.128, T.129, S.130, L.131, E.155, I.206 22 PLIP interactions: 10 interactions with chain C, 12 interactions with chain D Hydrophobic interactions: C:H.77, C:Y.78, D:F.26, D:I.29, D:T.129, D:L.131, D:I.206, D:I.206 Hydrogen bonds: C:G.35, C:H.77, C:H.77, C:H.77, C:G.79, C:S.80, C:S.80, C:S.80, D:Y.100, D:G.128, D:T.129, D:T.129, D:S.130, D:S.130

2 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.2: 10 residues within 4Å: Chain A: K.69, N.70, T.72, L.87 Chain B: V.9, R.36, N.40, N.41, V.42, L.43 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.41, B:N.41, B:N.41, B:N.40 Hydrophobic interactions: B:N.40 NAG-NAG-BMA-MAN.5: 7 residues within 4Å: Chain C: N.70, T.72, L.87 Chain D: V.9, N.40, N.41, L.43 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.41

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 2 residues within 4Å: Chain B: Y.92, N.94 No protein-ligand interaction detected (PLIP) NAG.6: 2 residues within 4Å: Chain D: Y.92, N.94 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.94, D:N.94

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baldwin, E.T. et al., Crystal structures of native and inhibited forms of human cathepsin D: implications for lysosomal targeting and drug design. Proc.Natl.Acad.Sci.USA (1993)

Release Date

1994-01-31

Peptides

CATHEPSIN D: AC
CATHEPSIN D: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

CATHEPSIN D

CATHEPSIN D

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