SMTL ID : 5veo.1

Murine ectonucleotide pyrophosphatase / phosphodiesterase 5 (ENPP5, NPP5), inactive (T72A), in complex with AMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[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-MAN.1: 5 residues within 4Å: Chain A: P.277, N.278, D.307, E.308, W.310 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- FUC: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-FUC.2: 5 residues within 4Å: Chain A: F.82, N.87, K.88, S.89 Ligands: PEG.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.89 Water bridges: A:S.89

3 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain A: D.177, H.181, H.225, M.227, H.325 Ligands: AMP.16 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.177, A:D.177, A:H.181, A:H.325, AMP.16 ZN.4: 9 residues within 4Å: Chain A: D.22, G.23, A.58, H.62, D.177, D.224, H.225, H.325 Ligands: AMP.16 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.22, A:D.22, A:D.224, A:D.224, A:H.225 ZN.5: 4 residues within 4Å: Chain A: E.145, E.174, D.178 Ligands: AMP.16 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.145, A:D.178, H2O.1, H2O.1, H2O.14

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

NAG.6: 6 residues within 4Å: Chain A: A.353, M.354, N.355, D.358, N.380 Ligands: EDO.10 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.353 Water bridges: A:K.351, A:N.355, A:N.355, A:N.355, A:N.355 NAG.7: 7 residues within 4Å: Chain A: L.69, F.70, N.73, H.292, P.373, H.374, N.375 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.73, A:N.375 Water bridges: A:N.73, A:H.374 NAG.8: 2 residues within 4Å: Chain A: N.144, S.146 4 PLIP interactions: 4 interactions with chain A Water bridges: A:N.144, A:N.144, A:N.144, A:N.144 NAG.9: 3 residues within 4Å: Chain A: N.315, K.316, S.317 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.317, A:S.317 Water bridges: A:K.316

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.10: 9 residues within 4Å: Chain A: T.51, N.52, V.53, F.70, N.329, N.355, S.356, T.357 Ligands: NAG.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.356, A:S.356, A:T.357 Water bridges: A:N.329, A:N.355 EDO.11: 5 residues within 4Å: Chain A: D.239, R.240, Y.241, L.242, D.243 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.240

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.12: 4 residues within 4Å: Chain A: Y.30, K.31, V.32, P.33 No protein-ligand interaction detected (PLIP)

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.13: 6 residues within 4Å: Chain A: F.82, S.89, T.248, I.250, L.259 Ligands: NAG-NAG-BMA-MAN-FUC.2 No protein-ligand interaction detected (PLIP) PEG.14: 7 residues within 4Å: Chain A: D.83, I.85, L.86, K.101, E.104, E.105, R.298 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.105 Water bridges: A:D.83, A:D.83, A:K.101, A:E.105 PEG.15: 4 residues within 4Å: Chain A: P.35, H.36, Y.39, K.209 No protein-ligand interaction detected (PLIP)

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.16: 23 residues within 4Å: Chain A: D.22, K.57, A.58, Y.59, N.79, L.92, M.95, I.97, Y.98, P.126, Y.143, E.145, Y.172, E.174, D.177, D.178, H.181, D.224, H.225, H.325 Ligands: ZN.3, ZN.4, ZN.5 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:A.58, A:Y.59, A:N.79, A:Y.98, A:D.178 Salt bridges: A:H.225, A:H.325 pi-Stacking: A:Y.143, A:Y.143 AMP.17: 2 residues within 4Å: Chain A: E.262, G.263 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gorelik, A. et al., A key tyrosine substitution restricts nucleotide hydrolysis by the ectoenzyme NPP5. FEBS J. (2017)

Release Date

2017-09-20

Peptides

Ectonucleotide pyrophosphatase/phosphodiesterase family member 5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ectonucleotide pyrophosphatase/phosphodiesterase family member 5