SMTL ID : 1nd6.3 (2 other biounits)

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 2.40 Å

Oligo State

homo-tetramer

Ligands

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

NAG-NAG-MAN-MAN.1: 3 residues within 4Å: Chain A: V.186, H.187, N.188 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.2: 6 residues within 4Å: Chain A: N.272, L.274, Y.299, N.301, E.302, Y.308 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.308

1 x NAG- NAG- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG-MAN-MAN-MAN.3: 5 residues within 4Å: Chain B: N.272, L.274, N.301, E.302, Y.308 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-MAN.4: 6 residues within 4Å: Chain C: N.272, L.274, P.277, N.301, E.302, Y.308 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-MAN-MAN-MAN.5: 6 residues within 4Å: Chain D: N.272, L.274, P.277, N.301, E.302, Y.308 No protein-ligand interaction detected (PLIP)

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 6 residues within 4Å: Chain A: R.11, H.12, R.15, R.79, H.257, D.258 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.258, A:D.258 Water bridges: A:R.15, A:D.179 Salt bridges: A:R.11, A:H.12, A:R.15, A:R.79, A:H.257 PO4.9: 6 residues within 4Å: Chain B: R.11, H.12, R.15, R.79, H.257, D.258 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.258 Water bridges: B:R.15 Salt bridges: B:R.11, B:H.12, B:R.15, B:R.79, B:H.257 PO4.12: 6 residues within 4Å: Chain C: R.11, H.12, R.15, R.79, H.257, D.258 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:D.258, C:D.258, C:D.258 Salt bridges: C:R.11, C:H.12, C:R.15, C:R.79, C:H.257 PO4.15: 7 residues within 4Å: Chain D: R.11, H.12, R.15, I.18, R.79, H.257, D.258 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:D.258 Salt bridges: D:R.11, D:H.12, D:R.15, D:R.79, D:H.257

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

1PE.7: 8 residues within 4Å: Chain A: S.117, E.118, D.119, Q.120, F.126, N.128, W.336 Chain D: K.161 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.120 1PE.11: 7 residues within 4Å: Chain B: S.117, E.118, D.119, Q.120, F.126, N.128, W.336 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.120, B:N.128 1PE.13: 7 residues within 4Å: Chain C: S.117, D.119, Q.120, F.126, N.128, V.230, W.336 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.120 1PE.16: 8 residues within 4Å: Chain D: S.117, E.118, D.119, Q.120, F.126, N.128, W.336, S.337 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.120, D:N.128 Water bridges: D:S.337, D:S.337

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

NAG.8: 3 residues within 4Å: Chain B: V.186, H.187, N.188 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.186, B:N.188 NAG.14: 2 residues within 4Å: Chain D: V.186, N.188 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:V.186, D:N.188

1 x GLY: GLYCINE(Non-covalent)

GLY.10: 4 residues within 4Å: Chain B: H.305, E.306, P.307, Y.308 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.306, B:E.306, B:P.307 Salt bridges: B:H.305

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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

prostatic acid phosphatase

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