SMTL ID : 2je4.1

Atomic-resolution crystal structure of chemically-synthesized HIV-1 protease in complex with JG-365

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.07 Å

Oligo State

homo-dimer

Ligands

1 x SER- LEU- ASN- JG3- ILE- VME: INHIBITOR MOLECULE JG365(Non-covalent)

SER-LEU-ASN-JG3-ILE-VME.1: 27 residues within 4Å: Chain A: R.8, D.25, G.27, A.28, D.29, D.30, I.47, G.48, G.49, I.50, V.82, I.84 Chain B: R.8, L.23, D.25, G.27, A.28, D.29, D.30, V.32, I.47, G.48, G.49, I.50, P.81, V.82, I.84 35 PLIP interactions: 18 interactions with chain B, 17 interactions with chain A Hydrophobic interactions: B:L.23, B:A.28, B:V.32, B:P.81, B:V.82, B:I.84, A:V.82 Hydrogen bonds: B:R.8, B:G.27, B:G.27, B:D.29, B:G.48, B:G.48, A:G.27, A:D.29, A:D.29, A:D.30, A:D.30, A:D.30, A:D.30, A:G.48, A:G.48 Water bridges: B:I.50, B:I.50, B:I.50, B:I.50, B:I.50, B:I.50, A:K.45, A:K.45, A:K.45, A:K.45, A:I.50, A:I.50 Salt bridges: A:D.25

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 3 residues within 4Å: Chain A: W.42, P.44, K.55 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.44 Salt bridges: A:K.55 ACT.3: 3 residues within 4Å: Chain A: E.21, V.82, N.83 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.21 Hydrogen bonds: A:E.21, A:N.83, A:N.83 ACT.10: 1 residues within 4Å: Chain B: K.55 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.55 ACT.11: 2 residues within 4Å: Chain B: R.14, K.70 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.70

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: F.99 Chain B: H.69 Ligands: SO4.13 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:H.69, A:F.99 Water bridges: A:F.99, A:F.99 GOL.5: 2 residues within 4Å: Chain A: T.12, T.67 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.12 Water bridges: A:L.10, A:L.10, A:T.12, A:T.12, A:T.12, A:T.12 GOL.6: 1 residues within 4Å: Chain A: Q.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.2

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 2 residues within 4Å: Chain A: P.1, H.69 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.69 SO4.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.9: 0 residues within 4Å: (No contacts) 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.14, A:R.14 SO4.12: 4 residues within 4Å: Chain B: I.15, G.16, G.17, P.63 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.16, B:G.17 SO4.13: 3 residues within 4Å: Chain B: P.1, H.69 Ligands: GOL.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.1 Salt bridges: B:H.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johnson, E.C.B. et al., Modular Total Chemical Synthesis of a Human Immunodeficiency Virus Type 1 Protease. J.Am.Chem.Soc. (2007)

Release Date

2007-08-28

Peptides

PROTEASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PROTEASE