SMTL ID : 7pbb.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: D.33, H.35, D.82, N.242, 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.8: 6 residues within 4Å: Chain B: D.33, H.35, D.82, N.242, S.517 Ligands: ZN.9 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.33, B:H.35, B:D.82, H2O.14, H2O.14 ZN.9: 6 residues within 4Å: Chain B: D.33, D.82, N.114, H.217, H.240 Ligands: ZN.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.82, B:H.217, B:H.240, H2O.14

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.3, H2O.9 CA.10: 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.17, H2O.23

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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.69 Water bridges: A:R.106 pi-Cation interactions: A:F.62 DMS.11: 7 residues within 4Å: Chain B: F.62, V.65, Q.66, R.69, A.104, L.105, R.106 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.69 Water bridges: B:R.106 pi-Cation interactions: B:F.62

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: Q.85, F.90, D.118, N.119, N.183, N.368, D.519, N.523 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.85, A:D.118, A:N.119, A:N.183, A:N.368, A:N.523 Water bridges: A:R.371 GOL.6: 8 residues within 4Å: Chain A: S.46, K.47, A.409, P.413, F.414, G.415, Q.520, I.522 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.47 Water bridges: A:G.415, A:Q.520 GOL.12: 8 residues within 4Å: Chain B: Q.85, F.90, D.118, N.119, N.183, N.368, D.519, N.523 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.85, B:D.118, B:N.119, B:N.183, B:N.368, B:N.523 Water bridges: B:R.371 GOL.13: 8 residues within 4Å: Chain B: S.46, K.47, A.409, P.413, F.414, G.415, Q.520, I.522 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.47 Water bridges: B:G.415, B:Q.520

2 x CFF: CAFFEINE(Non-covalent)

CFF.7: 6 residues within 4Å: Chain A: N.387, G.389, G.390, F.414, F.497, D.503 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.387 pi-Stacking: A:F.414, A:F.414, A:F.497 CFF.14: 6 residues within 4Å: Chain B: N.387, G.389, G.390, F.414, F.497, D.503 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.387 pi-Stacking: B:F.414, 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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