SMTL ID : 4h2b.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: D.34, D.83, N.115, H.218, H.241 Ligands: ZN.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.83, A:H.218, A:H.241, H2O.2 ZN.2: 5 residues within 4Å: Chain A: D.34, H.36, D.83, S.518 Ligands: ZN.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.34, A:H.36, A:D.83, H2O.2, H2O.2 ZN.6: 6 residues within 4Å: Chain B: D.34, D.83, N.115, H.218, H.241 Ligands: ZN.7 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.83, B:H.218, B:H.241, H2O.17 ZN.7: 5 residues within 4Å: Chain B: D.34, H.36, D.83, S.518 Ligands: ZN.6 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.34, B:H.36, B:D.83, H2O.17, H2O.18

2 x 0XE: 5,6-dihydroxy-4-oxo-2-phenyl-4H-chromen-7-yl beta-D-glucopyranosiduronic acid(Non-covalent)

0XE.3: 10 residues within 4Å: Chain A: D.45, R.352, N.388, G.390, G.391, R.393, F.415, G.445, F.498, D.504 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:D.45, A:F.415 Hydrogen bonds: A:R.352, A:R.352, A:N.388, A:R.393, A:G.445, A:D.504 Water bridges: A:N.388, A:D.504 Salt bridges: A:R.352, A:R.393, A:R.393 pi-Stacking: A:F.415, A:F.498, A:F.498 pi-Cation interactions: A:R.393 0XE.8: 10 residues within 4Å: Chain B: D.45, R.352, N.388, G.390, G.391, R.393, F.415, G.445, F.498, D.504 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:D.45, B:F.415 Hydrogen bonds: B:R.352, B:R.352, B:N.388, B:R.393, B:G.445, B:D.504 Water bridges: B:N.388, B:D.504 Salt bridges: B:R.352, B:R.393, B:R.393 pi-Stacking: B:F.415, B:F.498, B:F.498 pi-Cation interactions: B:R.393

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 3 residues within 4Å: Chain A: N.211, D.235, G.296 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:N.211, A:D.235, A:G.296, H2O.3, H2O.7 CA.9: 3 residues within 4Å: Chain B: N.211, D.235, G.296 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:N.211, B:D.235, B:G.296, H2O.19, H2O.23

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

CL.5: 4 residues within 4Å: Chain A: G.220, F.221, E.222, S.242 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: G.220, F.221, E.222, S.242 Ligand excluded by PLIP

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
A

B
A

5'-nucleotidase