SMTL ID : 7l1p.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

1 x R2A: (2-{[3-(4-{2-[(3-{[3-(carboxymethyl)-5-methyl-1-benzofuran-2-yl]ethynyl}benzene-1-carbonyl)amino]ethyl}piperazine-1-carbonyl)phenyl]ethynyl}-5-methyl-1-benzofuran-3-yl)acetic acid(Non-covalent)

R2A.1: 35 residues within 4Å: Chain A: E.38, V.39, I.40, P.41, Q.46, E.47, A.49, Y.50, L.53, T.76, A.79, A.80, W.83, A.120, E.121, H.122, K.124, T.125, M.129 Chain B: E.38, Q.46, E.47, A.49, Y.50, L.53, T.76, A.79, A.80, W.83, A.120, E.121, H.122, K.124, T.125, M.129 32 PLIP interactions: 14 interactions with chain A, 18 interactions with chain B Hydrophobic interactions: A:Q.46, A:A.49, A:Y.50, A:L.53, A:T.76, A:A.79, A:A.80, A:K.124, A:T.125, B:Q.46, B:A.49, B:Y.50, B:L.53, B:T.76, B:A.79, B:A.80, B:K.124, B:T.125 Hydrogen bonds: A:E.121, A:H.122, A:K.124, A:T.125, B:E.121, B:H.122, B:K.124, B:T.125, B:T.125 Salt bridges: A:H.122, B:E.38, B:H.122 pi-Stacking: B:Y.50 pi-Cation interactions: B:K.124

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

IOD.2: 4 residues within 4Å: Chain A: K.22, H.122, L.123, K.124 Ligand excluded by PLIP IOD.3: 3 residues within 4Å: Chain A: H.18, L.19, G.21 Ligand excluded by PLIP IOD.4: 7 residues within 4Å: Chain A: L.14, L.52, V.64, N.71, V.77, C.81, Q.88 Ligand excluded by PLIP IOD.8: 5 residues within 4Å: Chain B: K.22, V.39, H.122, L.123, K.124 Ligand excluded by PLIP IOD.9: 7 residues within 4Å: Chain B: L.14, L.52, V.64, N.71, V.77, C.81, Q.88 Ligand excluded by PLIP IOD.10: 3 residues within 4Å: Chain B: H.18, L.19, G.21 Ligand excluded by PLIP

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

SO4.5: 4 residues within 4Å: Chain A: T.17, H.18, N.106, 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 SO4.6: 6 residues within 4Å: Chain A: G.45, Q.46, S.74, T.75, T.76, V.77 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.45, A:S.74, A:T.75, A:T.76, A:T.76, A:T.76 SO4.7: 7 residues within 4Å: Chain A: I.11, Q.13, V.30, H.65, G.91, I.92, P.93 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.65 SO4.11: 5 residues within 4Å: Chain B: T.17, H.18, N.106, K.107, K.110 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.17, B:H.18 Salt bridges: B:H.18, B:K.107, B:K.110 SO4.12: 6 residues within 4Å: Chain B: L.19, E.20, K.110, I.113, G.114, R.117 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.20, B:I.113 SO4.13: 5 residues within 4Å: Chain B: G.45, S.74, T.75, T.76, V.77 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.45, B:S.74, B:S.74, B:T.75, B:T.76, B:T.76, B:T.76 SO4.14: 4 residues within 4Å: Chain B: I.11, V.30, H.65, I.92 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gorman, M.A. et al., HIV Integrase core domain in complex with inhibitor. To Be Published

Release Date

2021-12-22

Peptides

Integrase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Integrase

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