SMTL ID : 8ghr.1

Structure of human ENPP1 in complex with variable heavy domain VH27.2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

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

NAG-NAG.1: 2 residues within 4Å: Chain A: N.156, S.158 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 6 residues within 4Å: Chain A: L.82, K.318, P.398, N.399, N.400, R.621 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.82 Hydrogen bonds: A:K.318 NAG-NAG.3: 2 residues within 4Å: Chain B: N.156, S.158 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain B: L.82, K.318, P.398, N.399, N.400, R.621 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.82 Hydrogen bonds: B:K.318

4 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain A: D.191, H.195, H.239, H.350 Ligands: AMP.7 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.191, A:D.191, A:H.195, A:H.350, AMP.7 ZN.6: 5 residues within 4Å: Chain A: D.33, A.71, D.238, H.239 Ligands: AMP.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.33, A:D.33, A:D.238, A:H.239 ZN.11: 5 residues within 4Å: Chain B: D.191, H.195, H.239, H.350 Ligands: AMP.13 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.191, B:D.191, B:H.195, B:H.350, AMP.13 ZN.12: 5 residues within 4Å: Chain B: D.33, A.71, D.238, H.239 Ligands: AMP.13 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.33, B:D.33, B:D.238, B:H.239

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.7: 15 residues within 4Å: Chain A: D.33, A.71, F.72, N.92, L.105, K.110, P.138, Y.155, Y.186, D.191, H.195, H.239, H.350 Ligands: ZN.5, ZN.6 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:D.33, A:A.71, A:N.92, A:K.110, A:K.110, A:Y.155 Salt bridges: A:H.239, A:H.350 pi-Stacking: A:F.72, A:Y.155, A:Y.155 AMP.13: 15 residues within 4Å: Chain B: D.33, A.71, F.72, N.92, L.105, K.110, P.138, Y.155, Y.186, D.191, H.195, H.239, H.350 Ligands: ZN.11, ZN.12 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:D.33, B:A.71, B:N.92, B:K.110, B:K.110, B:Y.155 Salt bridges: B:H.239, B:H.350 pi-Stacking: B:F.72, B:Y.155, B:Y.155

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

NAG.8: 2 residues within 4Å: Chain A: N.100, P.278 No protein-ligand interaction detected (PLIP) NAG.9: 2 residues within 4Å: Chain A: N.292, R.296 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.292 NAG.14: 2 residues within 4Å: Chain B: N.100, P.278 No protein-ligand interaction detected (PLIP) NAG.15: 2 residues within 4Å: Chain B: N.292, R.296 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.292

2 x CA: CALCIUM ION(Non-covalent)

CA.10: 5 residues within 4Å: Chain A: D.615, D.617, D.619, R.621, D.623 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.615, A:D.619, A:R.621, A:D.623 CA.16: 5 residues within 4Å: Chain B: D.615, D.617, D.619, R.621, D.623 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.615, B:D.619, B:R.621, B:D.623

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Solomon, P.E. et al., Discovery of VH domains that allosterically inhibit ENPP1. Nat.Chem.Biol. (2024)

Release Date

2023-08-02

Peptides

Ectonucleotide pyrophosphatase/phosphodiesterase family member 1, secreted form, Immunoglobulin gamma-1 heavy chain fusion: AB
VH27: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Ectonucleotide pyrophosphatase/phosphodiesterase family member 1, secreted form, Immunoglobulin gamma-1 heavy chain fusion

VH27