SMTL ID : 6puy.1 (2 other biounits)

Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and INSTI XZ426 (compound 4d)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.80 Å

Oligo State

homo-octamer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.159, C.160, D.211 Ligands: MG.2, OZ1.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.159, A:D.211, H2O.1, H2O.1 MG.2: 5 residues within 4Å: Chain A: D.159, E.247, N.250 Ligands: MG.1, OZ1.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.159, A:E.247, A:E.247, H2O.8 MG.6: 5 residues within 4Å: Chain G: D.159, C.160, D.211 Ligands: MG.7, OZ1.9 4 PLIP interactions: 2 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.159, G:D.211, H2O.9, H2O.9 MG.7: 5 residues within 4Å: Chain G: D.159, E.247, N.250 Ligands: MG.6, OZ1.9 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.159, G:E.247, G:E.247, H2O.15

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.107, H.111, C.135, C.138 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.107, A:H.111, A:C.135, A:C.138 ZN.5: 4 residues within 4Å: Chain B: H.107, H.111, C.135, C.138 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.107, B:H.111, B:C.135, B:C.138 ZN.8: 4 residues within 4Å: Chain G: H.107, H.111, C.135, C.138 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:H.107, G:H.111, G:C.135, G:C.138 ZN.10: 4 residues within 4Å: Chain H: H.107, H.111, C.135, C.138 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:H.107, H:H.111, H:C.135, H:C.138

2 x OZ1: 4-amino-N-[(2,4-difluorophenyl)methyl]-1-hydroxy-6-(6-hydroxyhexyl)-2-oxo-1,2-dihydro-1,8-naphthyridine-3-carboxamide(Non-covalent)

OZ1.4: 13 residues within 4Å: Chain A: D.159, D.211, N.212, P.237, Y.238, P.240, Q.241, E.247 Chain E: G.4 Chain F: C.24, A.25 Ligands: MG.1, MG.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:N.212, A:Y.238, A:P.240 Hydrogen bonds: A:D.211 Water bridges: A:C.160, A:N.250 Halogen bonds: A:E.247 OZ1.9: 13 residues within 4Å: Chain G: D.159, D.211, N.212, P.237, Y.238, P.240, Q.241, E.247 Chain K: G.4 Chain L: C.24, A.25 Ligands: MG.6, MG.7 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:N.212, G:Y.238, G:P.240 Hydrogen bonds: G:D.211 Water bridges: G:C.160, G:N.250 Halogen bonds: G:E.247

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Passos, D.O. et al., Structural basis for strand-transfer inhibitor binding to HIV intasomes. Science (2020)

Release Date

2020-02-12

Peptides

Chimeric Sso7d and HIV-1 integrase: ABCDGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

G
A

H
B

I
C

J
D

Chimeric Sso7d and HIV-1 integrase

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