SMTL ID : 7oug.1

STLV-1 intasome:B56 in complex with the strand-transfer inhibitor raltegravir

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-2-mer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.12, H.16, C.39, C.42 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.12, A:H.16, A:C.39, A:C.42 ZN.2: 4 residues within 4Å: Chain B: H.12, H.16, C.39, C.42 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.12, B:H.16, B:C.39, B:C.42 ZN.6: 4 residues within 4Å: Chain F: H.12, H.16, C.39, C.42 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.12, F:H.16, F:C.39, F:C.42 ZN.7: 4 residues within 4Å: Chain G: H.12, H.16, C.39, C.42 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:H.12, G:H.16, G:C.39, G:C.42

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain B: D.69, D.126 Ligands: MG.4, RLT.5 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.69, B:D.126, H2O.1, H2O.1 MG.4: 4 residues within 4Å: Chain B: D.69, E.162 Ligands: MG.3, RLT.5 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.69, B:E.162, B:E.162, H2O.1 MG.8: 4 residues within 4Å: Chain G: D.69, D.126 Ligands: MG.9, RLT.10 4 PLIP interactions: 2 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.69, G:D.126, H2O.1, H2O.1 MG.9: 4 residues within 4Å: Chain G: D.69, E.162 Ligands: MG.8, RLT.10 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.69, G:E.162, G:E.162, H2O.1

2 x RLT: N-(4-fluorobenzyl)-5-hydroxy-1-methyl-2-(1-methyl-1-{[(5-methyl-1,3,4-oxadiazol-2-yl)carbonyl]amino}ethyl)-6-oxo-1,6-di hydropyrimidine-4-carboxamide(Non-covalent)

RLT.5: 13 residues within 4Å: Chain B: D.69, D.126, N.127, P.152, Y.153, P.155, T.156, E.162 Chain D: G.4 Chain E: C.27, A.28 Ligands: MG.3, MG.4 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:P.152, B:Y.153, B:P.155, B:P.155, B:E.162 Hydrogen bonds: B:E.162 Water bridges: B:I.70 pi-Stacking: B:Y.153 RLT.10: 13 residues within 4Å: Chain G: D.69, D.126, N.127, P.152, Y.153, P.155, T.156, E.162 Chain I: G.4 Chain J: C.27, A.28 Ligands: MG.8, MG.9 8 PLIP interactions: 8 interactions with chain G Hydrophobic interactions: G:P.152, G:Y.153, G:P.155, G:P.155, G:E.162 Hydrogen bonds: G:E.162 Water bridges: G:I.70 pi-Stacking: G:Y.153

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barski, M.S. et al., Structural basis for the inhibition of HTLV-1 integration inferred from cryo-EM deltaretroviral intasome structures. Nat Commun (2021)

Release Date

2021-08-18

Peptides

Integrase: ABFG
Isoform 3 of PC4 and SFRS1-interacting protein,Isoform Gamma-2 of Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform: CH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

F
A

G
B

C
F

H
C

Integrase

Isoform 3 of PC4 and SFRS1-interacting protein,Isoform Gamma-2 of Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform

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