SMTL ID : 6vqs.1

HIV Integrase Core domain (IN) in complex with [5-(3-fluorophenyl)-1-benzofuran-3-yl]acetic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: G.45, S.74, T.75, T.76, V.77 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.74, A:T.75, A:T.75, A:T.76, A:T.76, A:T.76 SO4.2: 3 residues within 4Å: Chain A: T.17, H.18, K.110 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:C.16, A:T.17, A:H.18 Salt bridges: A:H.18, A:K.110 SO4.3: 5 residues within 4Å: Chain A: Q.46, E.47, Y.50 Chain B: K.124 Ligands: R7J.8 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Salt bridges: B:H.122, B:K.124 Hydrogen bonds: A:Q.46, A:E.47 SO4.9: 5 residues within 4Å: Chain B: G.45, S.74, T.75, T.76, V.77 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.74, B:T.75, B:T.75, B:T.76, B:T.76, B:T.76 SO4.10: 3 residues within 4Å: Chain B: T.17, H.18, K.110 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:C.16, B:T.17, B:H.18 Salt bridges: B:H.18, B:K.110 SO4.11: 5 residues within 4Å: Chain A: K.124 Chain B: Q.46, E.47, Y.50 Ligands: R7J.16 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Salt bridges: A:H.122, A:K.124 Hydrogen bonds: B:Q.46, B:E.47

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

IOD.4: 3 residues within 4Å: Chain A: I.11, V.30, H.65 Ligand excluded by PLIP IOD.5: 3 residues within 4Å: Chain A: H.18, L.19, G.21 Ligand excluded by PLIP IOD.6: 5 residues within 4Å: Chain A: K.22, V.39, H.122, L.123, K.124 Ligand excluded by PLIP IOD.7: 2 residues within 4Å: Chain A: F.72, Q.88 Ligand excluded by PLIP IOD.12: 3 residues within 4Å: Chain B: I.11, V.30, H.65 Ligand excluded by PLIP IOD.13: 3 residues within 4Å: Chain B: H.18, L.19, G.21 Ligand excluded by PLIP IOD.14: 5 residues within 4Å: Chain B: K.22, V.39, H.122, L.123, K.124 Ligand excluded by PLIP IOD.15: 2 residues within 4Å: Chain B: F.72, Q.88 Ligand excluded by PLIP

2 x R7J: [5-(3-fluorophenyl)-1-benzofuran-3-yl]acetic acid(Non-covalent)

R7J.8: 15 residues within 4Å: Chain A: Q.46, A.49, Y.50, L.53, T.76, A.79, A.80, W.83 Chain B: Q.119, A.120, E.121, H.122, T.125, M.129 Ligands: SO4.3 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:T.125, A:A.49, A:L.53, A:T.76, A:A.79, A:A.80 Hydrogen bonds: B:E.121, B:H.122, B:T.125 Salt bridges: B:H.122 R7J.16: 15 residues within 4Å: Chain A: Q.119, A.120, E.121, H.122, T.125, M.129 Chain B: Q.46, A.49, Y.50, L.53, T.76, A.79, A.80, W.83 Ligands: SO4.11 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:T.125, B:A.49, B:L.53, B:T.76, B:A.79, B:A.80 Hydrogen bonds: A:E.121, A:H.122, A:T.125 Salt bridges: A:H.122

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gorman, M.A. et al., HIV Integrase Core domain (IN) in complex with [5-(3-fluorophenyl)-1-benzofuran-3-yl]acetic acid. To Be Published

Release Date

2021-02-10

Peptides

Integrase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Integrase

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