SMTL ID : 4h1y.1

Human ecto-5'-nucleotidase (CD73): crystal form II (open) in complex with PSB11552

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.58 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: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.33, A:D.82, H2O.2, H2O.3, H2O.14 ZN.7: 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.25 ZN.8: 5 residues within 4Å: Chain B: D.33, H.35, D.82, S.517 Ligands: ZN.7 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.33, B:D.82, H2O.25, H2O.27, H2O.38

2 x 0YQ: 2,2'-[(2-{[2-({[(2S,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]carbonyl}amino)ethyl]amino}-2-oxoethyl)imino]diacetic acid (non-preferred name)(Non-covalent)

0YQ.3: 9 residues within 4Å: Chain A: R.351, N.387, G.389, G.390, R.392, F.414, G.444, F.497, D.503 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.387, A:R.392, A:D.503 Water bridges: A:G.444 Salt bridges: A:R.351, A:R.392, A:R.392 pi-Stacking: A:F.414, A:F.497 0YQ.9: 9 residues within 4Å: Chain B: R.351, N.387, G.389, G.390, R.392, F.414, G.444, F.497, D.503 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.387, B:R.392, B:D.503 Water bridges: B:G.444 Salt bridges: B:R.351, B:R.392, B:R.392 pi-Stacking: B:F.414, B:F.497

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 1 residues within 4Å: Chain A: K.461 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.461, A:K.461 GOL.10: 1 residues within 4Å: Chain B: K.461 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.461, B:K.461

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 4 residues within 4Å: Chain A: G.219, F.220, E.221, S.241 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain B: G.219, F.220, E.221, S.241 Ligand excluded by PLIP

2 x CA: CALCIUM ION(Non-covalent)

CA.6: 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.15 CA.12: 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.25, H2O.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Knapp, K. et al., Crystal Structure of the Human Ecto-5'-Nucleotidase (CD73): Insights into the Regulation of Purinergic Signaling. Structure (2012)

Release Date

2012-11-28

Peptides

5'-nucleotidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
P

B
P

5'-nucleotidase

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