SMTL ID : 3ec0.1

High Resolution HIV-2 Protease Structure in Complex with Antiviral Inhibitor GRL-06579A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.18 Å

Oligo State

homo-dimer

Ligands

1 x GRL: (3AS,5R,6AR)-HEXAHYDRO-2H-CYCLOPENTA[B]FURAN-5-YL (2S,3S)-3-HYDROXY-4-(4-(HYDROXYMETHYL)-N-ISOBUTYLPHENYLSULFONAMIDO)-1-PHENYLBUTAN-2-YLCARBAMATE(Non-covalent)

GRL.1: 25 residues within 4Å: Chain A: R.8, D.25, G.27, A.28, D.29, 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, V.47, G.48, G.49, I.50, I.82 Ligands: CL.22 20 PLIP interactions: 10 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:A.28, A:I.32, A:P.81, A:I.82, B:L.23, B:V.47, B:I.82 Hydrogen bonds: A:D.29, A:D.30, A:D.30, A:D.30, B:G.27, B:G.27, B:G.27, B:D.29, B:D.30 Water bridges: A:I.50, B:I.50 Salt bridges: A:D.25, B:D.25

6 x IMD: IMIDAZOLE(Non-covalent)

IMD.2: 4 residues within 4Å: Chain A: L.99 Chain B: P.1 Ligands: ZN.4, CL.9 No protein-ligand interaction detected (PLIP) IMD.3: 3 residues within 4Å: Chain A: Y.14, E.65 Ligands: ZN.6 No protein-ligand interaction detected (PLIP) IMD.11: 3 residues within 4Å: Chain B: E.21 Ligands: IMD.12, ZN.15 No protein-ligand interaction detected (PLIP) IMD.12: 5 residues within 4Å: Chain B: R.8, V.10, E.21 Ligands: IMD.11, ZN.15 No protein-ligand interaction detected (PLIP) IMD.13: 8 residues within 4Å: Chain B: D.30, I.46, M.76 Ligands: ZN.16, ZN.20, CL.21, CL.22, CL.26 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.45 IMD.14: 4 residues within 4Å: Chain B: W.6 Ligands: ZN.17, CL.24, CL.25 1 PLIP interactions: 1 interactions with chain B pi-Stacking: B:W.6

10 x ZN: ZINC ION(Non-covalent)

ZN.4: 3 residues within 4Å: Chain A: L.99 Ligands: IMD.2, CL.9 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:L.99, H2O.1, H2O.1 ZN.5: 1 residues within 4Å: Chain A: D.79 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.79, A:D.79, H2O.1, H2O.1 ZN.6: 2 residues within 4Å: Chain A: E.65 Ligands: IMD.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.65, A:E.65, H2O.1 ZN.7: 3 residues within 4Å: Chain A: E.63, K.70 Ligands: CL.8 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.63, H2O.1 ZN.15: 3 residues within 4Å: Chain B: E.21 Ligands: IMD.11, IMD.12 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.21, B:E.21 ZN.16: 5 residues within 4Å: Chain B: D.30 Ligands: IMD.13, ZN.20, CL.22, CL.26 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.30, H2O.4 ZN.17: 4 residues within 4Å: Chain B: W.6 Ligands: IMD.14, CL.24, CL.25 No protein-ligand interaction detected (PLIP) ZN.18: 2 residues within 4Å: Chain B: E.65 Ligands: CL.23 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.65, B:E.65, H2O.4, H2O.4, H2O.4 ZN.19: 1 residues within 4Å: Chain B: E.58 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.58, H2O.7 ZN.20: 6 residues within 4Å: Chain B: D.29, D.30 Ligands: IMD.13, ZN.16, CL.22, CL.26 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.30, B:D.30, H2O.4

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

CL.8: 3 residues within 4Å: Chain A: E.63, K.70 Ligands: ZN.7 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: L.99 Ligands: IMD.2, ZN.4 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain B: K.45, I.46 Ligands: IMD.13 Ligand excluded by PLIP CL.22: 6 residues within 4Å: Chain B: V.47, G.48 Ligands: GRL.1, IMD.13, ZN.16, ZN.20 Ligand excluded by PLIP CL.23: 3 residues within 4Å: Chain B: G.17, E.65 Ligands: ZN.18 Ligand excluded by PLIP CL.24: 7 residues within 4Å: Chain B: S.4, L.5, W.6, K.7 Ligands: IMD.14, ZN.17, CL.25 Ligand excluded by PLIP CL.25: 4 residues within 4Å: Chain B: K.7 Ligands: IMD.14, ZN.17, CL.24 Ligand excluded by PLIP CL.26: 5 residues within 4Å: Chain B: D.29, D.30 Ligands: IMD.13, ZN.16, ZN.20 Ligand excluded by PLIP

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

NA.10: 2 residues within 4Å: Chain A: N.40, N.41 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kovalevsky, A.Y. et al., Structural evidence for effectiveness of darunavir and two related antiviral inhibitors against HIV-2 protease. J.Mol.Biol. (2008)

Release Date

2008-09-16

Peptides

Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protease

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