SMTL ID : 3s45.1

wild-type HIV-2 protease with antiviral drug amprenavir

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

homo-dimer

Ligands

1 x NA: SODIUM ION(Non-functional Binders)

NA.1: 2 residues within 4Å: Chain A: N.40, N.41 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.40

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

CL.2: 3 residues within 4Å: Chain A: L.99 Ligands: IMD.3, ZN.5 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: K.45, I.46 Ligands: IMD.18 Ligand excluded by PLIP CL.10: 6 residues within 4Å: Chain B: D.30, V.47, G.48 Ligands: CL.14, IMD.18, ZN.21 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain B: G.17, E.65 Ligands: ZN.23 Ligand excluded by PLIP CL.12: 8 residues within 4Å: Chain B: S.4, L.5, W.6, K.7 Ligands: CL.13, CL.15, IMD.19, ZN.22 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain B: K.7 Ligands: CL.12, CL.15, IMD.19, ZN.22 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain B: D.29, D.30 Ligands: CL.10, IMD.18, ZN.21 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain B: K.7 Ligands: CL.12, CL.13, IMD.19, ZN.22 Ligand excluded by PLIP

6 x IMD: IMIDAZOLE(Non-covalent)

IMD.3: 4 residues within 4Å: Chain A: L.99 Chain B: P.1 Ligands: CL.2, ZN.5 No protein-ligand interaction detected (PLIP) IMD.4: 3 residues within 4Å: Chain A: Y.14, E.65 Ligands: ZN.7 No protein-ligand interaction detected (PLIP) IMD.16: 3 residues within 4Å: Chain B: E.21 Ligands: IMD.17, ZN.20 No protein-ligand interaction detected (PLIP) IMD.17: 4 residues within 4Å: Chain B: V.10, E.21 Ligands: IMD.16, ZN.20 No protein-ligand interaction detected (PLIP) IMD.18: 8 residues within 4Å: Chain B: D.30, K.45, I.46, M.76 Ligands: CL.9, CL.10, CL.14, ZN.21 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.46 IMD.19: 5 residues within 4Å: Chain B: W.6 Ligands: CL.12, CL.13, CL.15, ZN.22 1 PLIP interactions: 1 interactions with chain B pi-Stacking: B:W.6

7 x ZN: ZINC ION(Non-covalent)

ZN.5: 3 residues within 4Å: Chain A: L.99 Ligands: CL.2, IMD.3 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:L.99, H2O.2 ZN.6: 1 residues within 4Å: Chain A: D.79 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.79, A:D.79 ZN.7: 2 residues within 4Å: Chain A: E.65 Ligands: IMD.4 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.65, H2O.1, H2O.1 ZN.20: 3 residues within 4Å: Chain B: E.21 Ligands: IMD.16, IMD.17 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.21, B:E.21 ZN.21: 4 residues within 4Å: Chain B: D.30 Ligands: CL.10, CL.14, IMD.18 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.30 ZN.22: 5 residues within 4Å: Chain B: W.6 Ligands: CL.12, CL.13, CL.15, IMD.19 No protein-ligand interaction detected (PLIP) ZN.23: 2 residues within 4Å: Chain B: E.65 Ligands: CL.11 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.65, B:E.65, H2O.3, H2O.3

1 x 478: {3-[(4-AMINO-BENZENESULFONYL)-ISOBUTYL-AMINO]-1-BENZYL-2-HYDROXY-PROPYL}-CARBAMIC ACID TETRAHYDRO-FURAN-3-YL ESTER(Non-covalent)

478.8: 23 residues within 4Å: Chain A: D.25, G.27, A.28, D.30, I.32, G.48, G.49, I.50, P.81, I.82, I.84 Chain B: L.23, D.25, G.27, A.28, D.29, D.30, I.32, G.48, G.49, I.50, I.82, I.84 21 PLIP interactions: 10 interactions with chain A, 11 interactions with chain B Hydrophobic interactions: A:A.28, A:I.32, A:I.50, A:P.81, A:I.82, A:I.84, B:L.23, B:I.82, B:I.84 Hydrogen bonds: A:D.30, A:D.30, B:G.27, B:G.27, B:G.27, B:D.29, B:D.30, B:D.30 Water bridges: A:I.50, B:I.50 Salt bridges: A:D.25, B:D.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tie, Y. et al., Critical differences in HIV-1 and HIV-2 protease specificity for clinical inhibitors. Protein Sci. (2012)

Release Date

2012-03-21

Peptides

Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protease

Related Entries With Identical Sequence