SMTL ID : 6tve.1

Unliganded human CD73 (5'-nucleotidase) in the open state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.05 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: N.210, K.211, D.234, G.295, N.296 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.12 CA.15: 5 residues within 4Å: Chain B: N.210, K.211, D.234, G.295, N.296 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:N.210, B:D.234, B:G.295, H2O.30, H2O.38

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 7 residues within 4Å: Chain A: D.33, D.82, N.114, H.115, H.217, H.240 Ligands: ZN.3 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.3: 8 residues within 4Å: Chain A: D.33, H.35, D.82, H.115, H.217, H.240, 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.2, H2O.2 ZN.16: 7 residues within 4Å: Chain B: D.33, D.82, N.114, H.115, H.217, H.240 Ligands: ZN.17 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.82, B:H.217, B:H.240, H2O.28 ZN.17: 8 residues within 4Å: Chain B: D.33, H.35, D.82, H.115, H.217, H.240, S.517 Ligands: ZN.16 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.33, B:H.35, B:D.82, H2O.28, H2O.28

16 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 Ligand excluded by PLIP DMS.6: 3 residues within 4Å: Chain A: P.146, S.149, Q.150 Ligand excluded by PLIP DMS.7: 4 residues within 4Å: Chain A: Y.331, Q.334, E.335, L.336 Ligand excluded by PLIP DMS.8: 6 residues within 4Å: Chain A: N.242, Y.278, A.279, F.280, N.496, N.500 Ligand excluded by PLIP DMS.9: 9 residues within 4Å: Chain A: R.37, D.44, S.45, S.46, F.280, F.414, G.415, G.416, N.496 Ligand excluded by PLIP DMS.11: 6 residues within 4Å: Chain A: M.532, V.534, I.535, Y.536, P.537 Chain B: N.367 Ligand excluded by PLIP DMS.13: 10 residues within 4Å: Chain A: I.141, S.142, A.143, I.151, S.152, G.153, L.154, Y.155, L.156, P.157 Ligand excluded by PLIP DMS.14: 9 residues within 4Å: Chain A: E.540, G.541, R.542, K.544 Chain B: H.453, E.540, G.541, K.544 Ligands: DMS.28 Ligand excluded by PLIP DMS.18: 7 residues within 4Å: Chain B: F.62, V.65, Q.66, R.69, A.104, L.105, R.106 Ligand excluded by PLIP DMS.20: 3 residues within 4Å: Chain B: P.146, S.149, Q.150 Ligand excluded by PLIP DMS.21: 4 residues within 4Å: Chain B: Y.331, Q.334, E.335, L.336 Ligand excluded by PLIP DMS.22: 6 residues within 4Å: Chain B: N.242, Y.278, A.279, F.280, N.496, N.500 Ligand excluded by PLIP DMS.23: 9 residues within 4Å: Chain B: R.37, D.44, S.45, S.46, F.280, F.414, G.415, G.416, N.496 Ligand excluded by PLIP DMS.25: 6 residues within 4Å: Chain A: N.367 Chain B: M.532, V.534, I.535, Y.536, P.537 Ligand excluded by PLIP DMS.27: 10 residues within 4Å: Chain B: I.141, S.142, A.143, I.151, S.152, G.153, L.154, Y.155, L.156, P.157 Ligand excluded by PLIP DMS.28: 9 residues within 4Å: Chain A: H.453, E.540, G.541, K.544 Chain B: E.540, G.541, R.542, K.544 Ligands: DMS.14 Ligand excluded by PLIP

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 11 residues within 4Å: Chain A: Q.85, F.90, D.118, N.119, N.183, N.368, R.371, D.519, N.523, V.524, T.527 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.85, A:N.119, A:N.183, A:N.368, A:D.519, A:D.519 Water bridges: A:R.371, A:R.371, A:N.523 GOL.10: 4 residues within 4Å: Chain A: Y.93, K.323, W.324, K.327 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.323 GOL.12: 6 residues within 4Å: Chain A: V.75, L.76, D.108, P.162, V.163, G.164 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.75, A:P.162, A:G.164 Water bridges: A:R.69, A:V.75, A:P.162 GOL.19: 11 residues within 4Å: Chain B: Q.85, F.90, D.118, N.119, N.183, N.368, R.371, D.519, N.523, V.524, T.527 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Q.85, B:N.119, B:N.183, B:N.368, B:D.519, B:D.519 Water bridges: B:R.371, B:R.371, B:N.523 GOL.24: 4 residues within 4Å: Chain B: Y.93, K.323, W.324, K.327 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.323 GOL.26: 6 residues within 4Å: Chain B: V.75, L.76, D.108, P.162, V.163, G.164 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:V.75, B:P.162, B:G.164 Water bridges: B:R.69, B:V.75, B:P.162

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bhattarai, S. et al., 2-Substituted alpha , beta-Methylene-ADP Derivatives: Potent Competitive Ecto-5'-nucleotidase (CD73) Inhibitors with Variable Binding Modes. J.Med.Chem. (2020)

Release Date

2020-02-19

Peptides

5'-nucleotidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
P

B
P

5'-nucleotidase

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