- 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)
- 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 PLIPCL.9: 3 residues within 4Å:- Chain A: L.99
- Ligands: IMD.2, ZN.4
Ligand excluded by PLIPCL.21: 3 residues within 4Å:- Chain B: K.45, I.46
- Ligands: IMD.13
Ligand excluded by PLIPCL.22: 6 residues within 4Å:- Chain B: V.47, G.48
- Ligands: GRL.1, IMD.13, ZN.16, ZN.20
Ligand excluded by PLIPCL.23: 3 residues within 4Å:- Chain B: G.17, E.65
- Ligands: ZN.18
Ligand excluded by PLIPCL.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 PLIPCL.25: 4 residues within 4Å:- Chain B: K.7
- Ligands: IMD.14, ZN.17, CL.24
Ligand excluded by PLIPCL.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)
- 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
AB
B
- 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)
- 6 x IMD: IMIDAZOLE(Non-covalent)
- 10 x ZN: ZINC ION(Non-covalent)
- 8 x CL: CHLORIDE ION(Non-functional Binders)
- 1 x NA: SODIUM ION(Non-functional Binders)
- 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
AB
B