SMTL ID : 7pb5.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.28 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: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.33, A:D.82, H2O.1, H2O.1, H2O.2 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.2 ZN.7: 5 residues within 4Å: Chain B: D.33, H.35, D.82, S.517 Ligands: ZN.8 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.33, B:D.82, H2O.19, H2O.19, H2O.20 ZN.8: 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.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.7 CA.9: 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.25

4 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.5: 5 residues within 4Å: Chain A: R.106, Y.107, D.108, K.133, F.134 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.103, A:D.108 GOL.10: 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 GOL.11: 5 residues within 4Å: Chain B: R.106, Y.107, D.108, K.133, F.134 2 PLIP interactions: 2 interactions with chain B Water bridges: B:N.103, B:D.108

2 x U: URIDINE-5'-MONOPHOSPHATE(Non-covalent)

U.6: 9 residues within 4Å: Chain A: R.351, N.387, G.389, G.390, R.392, F.414, G.444, F.497, D.503 24 PLIP interactions: 12 interactions with chain A, 12 interactions with chain B Hydrogen bonds: A:N.387, A:R.392, A:G.444, A:D.503, B:N.387, B:R.392, B:G.444, B:D.503 Water bridges: A:R.351, A:R.351, A:R.351, A:D.503, B:R.351, B:R.351, B:R.351, B:D.503 Salt bridges: A:R.351, A:R.392, B:R.351, B:R.392 pi-Stacking: A:F.414, A:F.497, B:F.414, B:F.497 U.12: 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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