SMTL ID : 1nd5.1 (1 other biounit)

Crystal Structures of Human Prostatic Acid Phosphatase in Complex with a Phosphate Ion and alpha-Benzylaminobenzylphosphonic Acid Update the Mechanistic Picture and Offer New Insights into Inhibitor Design

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-trimer

Ligands

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG-NAG.1: 3 residues within 4Å: Chain A: V.186, H.187, N.188 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 6 residues within 4Å: Chain A: N.272, L.274, P.277, N.301, E.302, Y.308 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.308 NAG-NAG.3: 6 residues within 4Å: Chain B: N.272, L.274, P.277, N.301, E.302, Y.308 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain C: N.272, L.274, N.301, E.302, Y.308 No protein-ligand interaction detected (PLIP)

3 x 2BF: ALPHA-BENZYL-AMINOBENZYL-PHOSPHONIC ACID(Non-covalent)

2BF.5: 14 residues within 4Å: Chain A: R.11, H.12, R.15, I.18, R.79, Y.123, L.124, F.171, W.174, S.175, H.257, D.258, T.259 Ligands: 1PE.7 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.18, A:Y.123, A:F.171, A:H.257, A:T.259 Hydrogen bonds: A:R.11, A:R.15, A:R.79, A:H.257, A:D.258, A:D.258 pi-Cation interactions: A:H.257 2BF.10: 12 residues within 4Å: Chain B: R.11, H.12, R.15, I.18, R.79, Y.123, F.171, S.175, H.257, D.258, T.259 Ligands: 1PE.12 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.18, B:F.171, B:H.257 Hydrogen bonds: B:R.11, B:R.15, B:R.79, B:H.257, B:D.258, B:D.258 pi-Stacking: B:H.257 2BF.13: 14 residues within 4Å: Chain C: R.11, H.12, R.15, I.18, R.79, Y.123, L.124, F.171, W.174, S.175, H.257, D.258, T.259 Ligands: 1PE.15 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:I.18, C:Y.123, C:F.171, C:H.257, C:T.259 Hydrogen bonds: C:R.11, C:R.15, C:R.79, C:H.257, C:D.258 pi-Cation interactions: C:H.257

7 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.6: 7 residues within 4Å: Chain A: S.117, E.118, D.119, Q.120, F.126, N.128, W.336 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.120, A:N.128 1PE.7: 9 residues within 4Å: Chain A: Y.123, L.124, P.125, R.127, E.136, F.171, L.214, T.259 Ligands: 2BF.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.127 1PE.8: 1 residues within 4Å: Chain A: K.176 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.176 1PE.11: 6 residues within 4Å: Chain B: S.117, E.118, D.119, Q.120, N.128, W.336 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.120 1PE.12: 5 residues within 4Å: Chain B: Y.123, P.125, R.127, F.171 Ligands: 2BF.10 No protein-ligand interaction detected (PLIP) 1PE.14: 7 residues within 4Å: Chain A: K.161 Chain C: S.117, D.119, Q.120, F.126, N.128, W.336 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.120 1PE.15: 8 residues within 4Å: Chain C: Y.123, L.124, P.125, R.127, E.136, F.171, S.210 Ligands: 2BF.13 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.127, C:S.210

1 x NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-covalent)

NDG.9: 3 residues within 4Å: Chain B: V.186, H.187, N.188 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.188

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ortlund, E. et al., Crystal structures of human prostatic acid phosphatase in complex with a phosphate ion and alpha-benzylaminobenzylphosphonic acid update the mechanistic picture and offer new insights into inhibitor design. Biochemistry (2003)

Release Date

2002-12-20

Peptides

prostatic acid phosphatase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

prostatic acid phosphatase

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