SMTL ID : 7adu.1

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and the INSTI XZ440 (compound 5j)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.62 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.131, D.188 Ligands: MG.2, R7K.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.131, A:D.188, H2O.1, H2O.2 MG.2: 5 residues within 4Å: Chain A: D.131, E.224, N.227 Ligands: MG.1, R7K.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.131, A:E.224, A:E.224, H2O.7 MG.23: 4 residues within 4Å: Chain E: D.131, D.188 Ligands: MG.24, R7K.25 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.131, E:D.188, H2O.8, H2O.9 MG.24: 5 residues within 4Å: Chain E: D.131, E.224, N.227 Ligands: MG.23, R7K.25 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.131, E:E.224, E:E.224, H2O.14

2 x R7K: ~{N}-[[2,4-bis(fluoranyl)phenyl]methyl]-5-(hydroxymethyl)-1,4-bis(oxidanyl)-2-oxidanylidene-1,8-naphthyridine-3-carboxamide(Non-covalent)

R7K.3: 12 residues within 4Å: Chain A: D.131, D.188, P.217, Q.218, E.224 Chain C: G.4 Chain D: C.16, A.17 Ligands: MG.1, MG.2, SO4.8, MES.17 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.217, A:P.217 Water bridges: A:Y.132, A:N.227, A:R.332, A:R.332 Halogen bonds: A:E.224 R7K.25: 12 residues within 4Å: Chain E: D.131, D.188, P.217, Q.218, E.224 Chain G: G.4 Chain H: C.16, A.17 Ligands: MG.23, MG.24, SO4.30, MES.39 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:P.217, E:P.217 Water bridges: E:Y.132, E:N.227, E:R.332, E:R.332 Halogen bonds: E:E.224

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: H.65, H.69, C.99, C.102 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.65, A:H.69, A:C.99, A:C.102 ZN.26: 4 residues within 4Å: Chain E: H.65, H.69, C.99, C.102 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.65, E:H.69, E:C.99, E:C.102

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

SO4.5: 4 residues within 4Å: Chain A: S.335, L.336, R.339 Chain E: K.231 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain A: P.118, D.119 Chain C: T.3 Ligand excluded by PLIP SO4.7: 4 residues within 4Å: Chain A: P.138, S.139, Q.140, K.244 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain A: G.190, A.191 Ligands: R7K.3, MES.17 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain A: H.341, K.342, H.360 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain A: G.21, H.22, Y.23 Ligand excluded by PLIP SO4.11: 7 residues within 4Å: Chain A: L.76, A.80, W.84, M.88, R.89 Chain H: A.7, T.8 Ligand excluded by PLIP SO4.12: 6 residues within 4Å: Chain A: R.337, R.339 Chain E: K.231, R.232, T.235 Chain H: C.16 Ligand excluded by PLIP SO4.18: 5 residues within 4Å: Chain B: K.222, R.225, S.261, P.262, V.263 Ligand excluded by PLIP SO4.19: 2 residues within 4Å: Chain B: S.220, G.221 Ligand excluded by PLIP SO4.22: 2 residues within 4Å: Chain D: G.4, A.5 Ligand excluded by PLIP SO4.27: 4 residues within 4Å: Chain A: K.231 Chain E: S.335, L.336, R.339 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain E: P.118, D.119 Chain G: T.3 Ligand excluded by PLIP SO4.29: 4 residues within 4Å: Chain E: P.138, S.139, Q.140, K.244 Ligand excluded by PLIP SO4.30: 4 residues within 4Å: Chain E: G.190, A.191 Ligands: R7K.25, MES.39 Ligand excluded by PLIP SO4.31: 3 residues within 4Å: Chain E: H.341, K.342, H.360 Ligand excluded by PLIP SO4.32: 3 residues within 4Å: Chain E: G.21, H.22, Y.23 Ligand excluded by PLIP SO4.33: 7 residues within 4Å: Chain D: A.7, T.8 Chain E: L.76, A.80, W.84, M.88, R.89 Ligand excluded by PLIP SO4.34: 6 residues within 4Å: Chain A: K.231, R.232, T.235 Chain D: C.16 Chain E: R.337, R.339 Ligand excluded by PLIP SO4.40: 5 residues within 4Å: Chain F: K.222, R.225, S.261, P.262, V.263 Ligand excluded by PLIP SO4.41: 2 residues within 4Å: Chain F: S.220, G.221 Ligand excluded by PLIP SO4.44: 2 residues within 4Å: Chain H: G.4, A.5 Ligand excluded by PLIP

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 3 residues within 4Å: Chain A: S.165, T.166, S.167 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.167, A:S.167 GOL.14: 5 residues within 4Å: Chain A: R.117, Y.306, P.308 Chain C: C.6 Ligands: GOL.21 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.117, A:R.117, A:Y.306, A:Y.306 GOL.15: 5 residues within 4Å: Chain A: Q.63, L.82, Y.83 Chain E: P.280, F.281 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:Q.63, A:Y.83, E:F.281 GOL.16: 6 residues within 4Å: Chain A: K.342, L.358, D.359, H.360, L.361, G.362 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.342, A:L.361 Water bridges: A:T.345 GOL.20: 7 residues within 4Å: Chain A: L.295, Q.299 Chain B: Y.266, Q.270, G.274, I.275, D.276 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.275 GOL.21: 7 residues within 4Å: Chain A: V.263 Chain C: C.6, A.7, T.8 Chain D: C.11, A.12 Ligands: GOL.14 2 PLIP interactions: 2 interactions with chain A Water bridges: A:V.263, A:Y.306 GOL.35: 3 residues within 4Å: Chain E: S.165, T.166, S.167 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:S.167, E:S.167 GOL.36: 5 residues within 4Å: Chain E: R.117, Y.306, P.308 Chain G: C.6 Ligands: GOL.43 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.117, E:R.117, E:Y.306 GOL.37: 5 residues within 4Å: Chain A: P.280, F.281 Chain E: Q.63, L.82, Y.83 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:Q.63, E:Y.83, E:Y.83, A:F.281 GOL.38: 6 residues within 4Å: Chain E: K.342, L.358, D.359, H.360, L.361, G.362 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:K.342, E:L.361 Water bridges: E:T.345 GOL.42: 7 residues within 4Å: Chain E: L.295, Q.299 Chain F: Y.266, Q.270, G.274, I.275, D.276 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:I.275 GOL.43: 7 residues within 4Å: Chain E: V.263 Chain G: C.6, A.7, T.8 Chain H: C.11, A.12 Ligands: GOL.36 2 PLIP interactions: 2 interactions with chain E Water bridges: E:V.263, E:Y.306

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.17: 8 residues within 4Å: Chain A: D.188, Q.189, G.190, P.214, Y.215, R.332 Ligands: R7K.3, SO4.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.189, A:Y.215 Water bridges: A:H.216, A:H.216 MES.39: 8 residues within 4Å: Chain E: D.188, Q.189, G.190, P.214, Y.215, R.332 Ligands: R7K.25, SO4.30 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:Q.189, E:Y.215 Water bridges: E:H.216, E:H.216

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Smith, S.J. et al., HIV-1 Integrase Inhibitors with Modifications That Affect Their Potencies against Drug Resistant Integrase Mutants. Acs Infect Dis. (2021)

Release Date

2021-03-24

Peptides

Integrase: ABEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
A

F
B

Integrase

Related Entries With Identical Sequence