SMTL ID : 7pcp.1

Crystal structure of CD73 in complex with 5-iodouracil in the open form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.38 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: D.33, D.82, N.114, H.217, H.240 Ligands: ZN.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.82, A:H.217, A:H.240, H2O.2 ZN.2: 5 residues within 4Å: Chain A: D.33, H.35, D.82, S.517 Ligands: ZN.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.33, A:H.35, A:D.82, H2O.2, H2O.2 ZN.6: 6 residues within 4Å: Chain B: D.33, D.82, N.114, H.217, H.240 Ligands: ZN.7 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.82, B:H.217, B:H.240, H2O.21 ZN.7: 5 residues within 4Å: Chain B: D.33, H.35, D.82, S.517 Ligands: ZN.6 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.33, B:H.35, B:D.82, H2O.21, H2O.21

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.11 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.30

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 7 residues within 4Å: Chain A: F.62, V.65, Q.66, R.69, A.104, L.105, R.106 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.69 pi-Cation interactions: A:F.62 DMS.9: 7 residues within 4Å: Chain B: F.62, V.65, Q.66, R.69, A.104, L.105, R.106 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.69 pi-Cation interactions: B:F.62

2 x IUR: 5-IODOURACIL(Non-covalent)

IUR.5: 5 residues within 4Å: Chain A: N.387, G.389, G.390, F.414, F.497 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.387, A:G.389, A:R.392 pi-Stacking: A:F.414, A:F.497 IUR.10: 5 residues within 4Å: Chain B: N.387, G.389, G.390, F.414, F.497 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.387, B:G.389, B:R.392 pi-Stacking: B:F.414, 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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