SMTL ID : 6vka.1

HIV Integrase Core domain (IN) in complex with dimer-spanning ligand

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-dimer

Ligands

6 x IOD: IODIDE ION(Non-functional Binders)

IOD.1: 4 residues within 4Å: Chain A: K.24, H.124, L.125, K.126 Ligand excluded by PLIP IOD.2: 3 residues within 4Å: Chain A: H.20, L.21, G.23 Ligand excluded by PLIP IOD.9: 2 residues within 4Å: Chain A: K.139, R.140 Ligand excluded by PLIP IOD.10: 4 residues within 4Å: Chain B: K.24, H.124, L.125, K.126 Ligand excluded by PLIP IOD.11: 4 residues within 4Å: Chain B: G.35, H.136, K.141, A.149 Ligand excluded by PLIP IOD.17: 4 residues within 4Å: Chain B: H.20, L.21, E.22, G.23 Ligand excluded by PLIP

1 x QZV: 2,2'-{ethane-1,2-diylbis[oxyethane-2,1-diylcarbamoyl-4,1-phenyleneethyne-2,1-diyl(5-methyl-1-benzofuran-2,3-diyl)]}diacetic acid(Non-covalent)

QZV.3: 30 residues within 4Å: Chain A: Q.48, E.49, A.51, Y.52, L.55, T.78, A.81, A.82, W.85, A.122, E.123, H.124, K.126, T.127, M.131 Chain B: Q.48, E.49, A.51, Y.52, L.55, T.78, A.81, A.82, W.85, A.122, E.123, H.124, K.126, T.127, M.131 32 PLIP interactions: 17 interactions with chain A, 15 interactions with chain B Hydrophobic interactions: A:Q.48, A:E.49, A:A.51, A:Y.52, A:Y.52, A:L.55, A:T.78, A:A.81, A:A.82, A:T.127, B:Q.48, B:A.51, B:Y.52, B:L.55, B:T.78, B:A.81, B:A.82, B:T.127 Hydrogen bonds: A:E.49, A:E.123, A:H.124, A:T.127, A:T.127, B:E.123, B:E.123, B:H.124, B:K.126, B:T.127, B:T.127 Salt bridges: A:H.124, B:H.124 pi-Stacking: A:H.124

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

SO4.4: 4 residues within 4Å: Chain A: C.18, T.19, H.20, K.112 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.19, A:H.20 Salt bridges: A:H.20, A:K.112 SO4.5: 6 residues within 4Å: Chain A: T.46, G.47, Q.48, S.76, T.77, T.78 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.76, A:T.77, A:T.78, A:T.78, A:T.78 Water bridges: A:Q.48 SO4.6: 3 residues within 4Å: Chain A: P.62, K.64 Chain B: K.138 4 PLIP interactions: 4 interactions with chain B Water bridges: B:K.138, B:E.151, B:E.151 Salt bridges: B:K.138 SO4.7: 6 residues within 4Å: Chain A: P.43, E.45, G.47, Q.48, E.49, T.50 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.47, A:Q.48, A:E.49, A:E.49, A:T.50 SO4.8: 6 residues within 4Å: Chain A: E.40, Y.52, F.53, K.56 Chain B: E.40, K.56 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Water bridges: A:F.53, A:F.53, A:F.53, A:L.57, B:K.126 Salt bridges: A:K.56, B:K.56 SO4.12: 5 residues within 4Å: Chain B: C.18, T.19, H.20, N.108, K.112 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.19, B:H.20, B:N.108 Salt bridges: B:H.20, B:K.112 SO4.13: 6 residues within 4Å: Chain B: L.21, E.22, K.112, I.115, G.116, R.119 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.22, B:I.115 SO4.14: 5 residues within 4Å: Chain B: S.10, P.11, G.12, I.13, K.64 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.12 Salt bridges: B:K.64 SO4.15: 5 residues within 4Å: Chain B: G.47, S.76, T.77, T.78, V.79 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.47, B:S.76, B:S.76, B:T.77, B:T.78, B:T.78, B:T.78 Water bridges: B:Q.48, B:Q.48 SO4.16: 6 residues within 4Å: Chain A: E.40, K.56 Chain B: E.40, Y.52, F.53, K.56 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Water bridges: B:A.39, B:F.53, A:K.56 Salt bridges: B:K.56, A:K.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Scanlon, M. et al., HIV Integrase core domain (IN) in complex with dimeric spanning inhibitor. To Be Published

Release Date

2021-01-20

Peptides

Integrase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Integrase