SMTL ID : 7pba.1

Crystal structure of CD73 in complex with IMP in the open form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: D.33, H.35, D.82, S.517 Ligands: ZN.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.33, A:H.35, A:D.82, H2O.1, H2O.1 ZN.2: 6 residues within 4Å: Chain A: D.33, D.82, N.114, H.217, H.240 Ligands: ZN.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.82, A:H.217, A:H.240, H2O.1 ZN.6: 5 residues within 4Å: Chain B: D.33, H.35, D.82, S.517 Ligands: ZN.7 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.33, B:H.35, B:D.82, H2O.20, H2O.20 ZN.7: 6 residues within 4Å: Chain B: D.33, D.82, N.114, H.217, H.240 Ligands: ZN.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.82, B:H.217, B:H.240, H2O.20

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 3 residues within 4Å: Chain A: N.210, D.234, G.295 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:N.210, A:D.234, A:G.295, H2O.2, H2O.8 CA.8: 3 residues within 4Å: Chain B: N.210, D.234, G.295 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:N.210, B:D.234, B:G.295, H2O.20, H2O.27

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 10 residues within 4Å: Chain A: L.386, N.387, G.390, L.412, F.414, G.416, F.418, P.495, D.521 Ligands: IMP.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.387, A:N.387, A:D.521 Water bridges: A:G.415, A:T.417, A:N.496 GOL.9: 10 residues within 4Å: Chain B: L.386, N.387, G.390, L.412, F.414, G.416, F.418, P.495, D.521 Ligands: IMP.10 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.387, B:N.387, B:D.521 Water bridges: B:G.415, B:T.417, B:N.496

2 x IMP: INOSINIC ACID(Non-covalent)

IMP.5: 10 residues within 4Å: Chain A: R.351, N.387, G.389, G.390, R.392, F.414, G.444, F.497, D.503 Ligands: GOL.4 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:N.387, A:G.444, A:D.503 Water bridges: A:R.351, A:S.442, A:D.503 Salt bridges: A:R.351, A:R.392 pi-Stacking: A:F.414, A:F.414, A:F.497, A:F.497 IMP.10: 10 residues within 4Å: Chain B: R.351, N.387, G.389, G.390, R.392, F.414, G.444, F.497, D.503 Ligands: GOL.9 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:N.387, B:G.444, B:D.503 Water bridges: B:R.351, B:S.442, B:D.503 Salt bridges: B:R.351, B:R.392 pi-Stacking: B:F.414, B:F.414, B:F.497, B:F.497

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Scaletti, E. et al., Substrate binding modes of purine and pyrimidine nucleotides to human ecto-5'-nucleotidase (CD73) and inhibition by their bisphosphonic acid derivatives. Purinergic Signal (2021)

Release Date

2021-10-13

Peptides

5'-nucleotidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

5'-nucleotidase

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