SMTL ID : 6vx2.1

HIV Integrase core domain in complex with inhibitor (5-methyl-1-benzofuran-3-yl)acetic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

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

IOD.1: 1 residues within 4Å: Chain A: H.65 Ligand excluded by PLIP IOD.2: 2 residues within 4Å: Chain A: K.22, K.124 Ligand excluded by PLIP IOD.3: 2 residues within 4Å: Chain A: P.60 Chain B: K.136 Ligand excluded by PLIP IOD.4: 1 residues within 4Å: Chain A: F.90 Ligand excluded by PLIP IOD.5: 3 residues within 4Å: Chain A: H.18, L.19, G.21 Ligand excluded by PLIP IOD.6: 4 residues within 4Å: Chain A: L.52, V.64, C.81, Q.88 Ligand excluded by PLIP IOD.7: 4 residues within 4Å: Chain A: S.32, G.33, H.134, R.150 Ligand excluded by PLIP IOD.11: 1 residues within 4Å: Chain B: H.65 Ligand excluded by PLIP IOD.12: 2 residues within 4Å: Chain B: K.22, K.124 Ligand excluded by PLIP IOD.13: 2 residues within 4Å: Chain A: K.136 Chain B: P.60 Ligand excluded by PLIP IOD.14: 1 residues within 4Å: Chain B: F.90 Ligand excluded by PLIP IOD.15: 3 residues within 4Å: Chain B: H.18, L.19, G.21 Ligand excluded by PLIP IOD.16: 4 residues within 4Å: Chain B: L.52, V.64, C.81, Q.88 Ligand excluded by PLIP IOD.17: 4 residues within 4Å: Chain B: S.32, G.33, H.134, R.150 Ligand excluded by PLIP

2 x RQG: (5-methyl-1-benzofuran-3-yl)acetic acid(Non-covalent)

RQG.8: 11 residues within 4Å: Chain A: Q.46, A.49, Y.50, L.53, T.76, A.80 Chain B: A.120, E.121, H.122, T.125, M.129 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:T.125, A:L.53, A:T.76, A:A.80 Hydrogen bonds: B:E.121, B:H.122 Salt bridges: B:H.122 RQG.18: 11 residues within 4Å: Chain A: A.120, E.121, H.122, T.125, M.129 Chain B: Q.46, A.49, Y.50, L.53, T.76, A.80 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:T.125, B:L.53, B:T.76, B:A.80 Hydrogen bonds: A:E.121, A:H.122, A:T.125 Salt bridges: A:H.122

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

SO4.9: 3 residues within 4Å: Chain A: T.17, H.18, K.110 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.17, A:H.18 Salt bridges: A:H.18, A:K.110 SO4.10: 4 residues within 4Å: Chain A: G.45, S.74, T.75, T.76 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.45, A:T.75, A:T.76, A:T.76 SO4.19: 3 residues within 4Å: Chain B: T.17, H.18, K.110 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.17, B:T.17, B:H.18 Salt bridges: B:H.18, B:K.110 SO4.20: 4 residues within 4Å: Chain B: G.45, S.74, T.75, T.76 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.45, B:T.75, B:T.76, B:T.76, B:T.76

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gorman, M.A. et al., HIV Integrase core domain in complex with inhibitor (5-methyl-1-benzofuran-3-yl)acetic acid. To Be Published

Release Date

2021-02-24

Peptides

Integrase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Integrase