SMTL ID : 7p9r.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.41 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.3, H2O.3 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.3 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.22, H2O.22 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.22

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.1, H2O.7 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.21, H2O.26

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: F.62, V.65, Q.66, R.69, A.104, L.105, R.106 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.69 GOL.9: 7 residues within 4Å: Chain B: F.62, V.65, Q.66, R.69, A.104, L.105, R.106 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.69

2 x G: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

G.5: 9 residues within 4Å: Chain A: R.351, N.387, G.389, G.390, R.392, F.414, G.444, F.497, D.503 32 PLIP interactions: 16 interactions with chain A, 16 interactions with chain B Hydrogen bonds: A:N.387, A:G.444, A:D.503, B:N.387, B:G.444, B:D.503 Water bridges: A:R.351, A:R.351, A:N.496, A:F.497, A:D.503, A:D.503, B:R.351, B:R.351, B:N.496, B:F.497, B:D.503, B:D.503 Salt bridges: A:R.351, A:R.392, B:R.351, B:R.392 pi-Stacking: A:F.414, A:F.414, A:F.497, A:F.497, B:F.414, B:F.414, B:F.497, B:F.497 pi-Cation interactions: A:F.497, B:F.497 G.10: 9 residues within 4Å: Chain B: R.351, N.387, G.389, G.390, R.392, F.414, G.444, F.497, D.503 Protein-ligand interaction information (PLIP) not available

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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