SMTL ID : 4h2i.1

Human ecto-5'-nucleotidase (CD73): crystal form III (closed) in complex with AMPCP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: D.11, H.13, D.60 Ligands: ZN.2, A12.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.11, A:H.13, A:D.60, H2O.3 ZN.2: 7 residues within 4Å: Chain A: D.11, D.60, N.92, H.195, H.218 Ligands: ZN.1, A12.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.60, A:H.195, A:H.218 ZN.6: 5 residues within 4Å: Chain B: D.11, H.13, D.60 Ligands: ZN.7, A12.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.11, B:H.13, B:D.60, H2O.18 ZN.7: 7 residues within 4Å: Chain B: D.11, D.60, N.92, H.195, H.218 Ligands: ZN.6, A12.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.60, B:H.195, B:H.218

2 x A12: PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)

A12.3: 19 residues within 4Å: Chain A: D.11, H.13, D.60, N.92, H.93, L.159, H.218, N.220, R.329, N.365, G.367, G.368, R.370, F.392, G.422, F.475, D.481 Ligands: ZN.1, ZN.2 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:N.92, A:L.159, A:H.218, A:N.220, A:R.329, A:R.329, A:N.365, A:G.367, A:R.370, A:R.370, A:G.422, A:D.481 Water bridges: A:F.475, A:D.481 pi-Stacking: A:F.392, A:F.475 A12.8: 19 residues within 4Å: Chain B: D.11, H.13, D.60, N.92, H.93, L.159, H.218, N.220, R.329, N.365, G.367, G.368, R.370, F.392, G.422, F.475, D.481 Ligands: ZN.6, ZN.7 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:N.92, B:L.159, B:H.218, B:N.220, B:R.329, B:R.329, B:N.365, B:G.367, B:R.370, B:R.370, B:G.422, B:D.481 Water bridges: B:F.475 pi-Stacking: B:F.392, B:F.475

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

CL.4: 4 residues within 4Å: Chain A: G.197, F.198, E.199, S.219 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain B: G.197, F.198, E.199, S.219 Ligand excluded by PLIP

2 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain A: K.183, N.188, D.212, G.273 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:N.188, A:D.212, A:G.273, H2O.2, H2O.3 CA.10: 4 residues within 4Å: Chain B: K.183, N.188, D.212, G.273 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:N.188, B:D.212, B:G.273, H2O.17, H2O.18

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

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