SMTL ID : 6rwn.1

SIVrcm intasome in complex with dolutegravir

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.13, H.17, C.41, C.44 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.13, A:H.17, A:C.41, A:C.44 ZN.6: 4 residues within 4Å: Chain D: H.13, H.17, C.41, C.44 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.13, D:H.17, D:C.41, D:C.44 ZN.7: 4 residues within 4Å: Chain G: H.13, H.17, C.41, C.44 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:H.13, G:H.17, G:C.41, G:C.44 ZN.8: 4 residues within 4Å: Chain H: H.13, H.17, C.41, C.44 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:H.13, H:H.17, H:C.41, H:C.44 ZN.9: 4 residues within 4Å: Chain I: H.13, H.17, C.41, C.44 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:H.13, I:H.17, I:C.41, I:C.44 ZN.14: 4 residues within 4Å: Chain L: H.13, H.17, C.41, C.44 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:H.13, L:H.17, L:C.41, L:C.44 ZN.15: 4 residues within 4Å: Chain O: H.13, H.17, C.41, C.44 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:H.13, O:H.17, O:C.41, O:C.44 ZN.16: 4 residues within 4Å: Chain P: H.13, H.17, C.41, C.44 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:H.13, P:H.17, P:C.41, P:C.44

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 5 residues within 4Å: Chain A: D.117, N.118, P.143, Y.144 Ligands: DLU.3 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain I: D.117, N.118, P.143, Y.144 Ligands: DLU.11 Ligand excluded by PLIP

2 x DLU: (4R,12aS)-N-(2,4-difluorobenzyl)-7-hydroxy-4-methyl-6,8-dioxo-3,4,6,8,12,12a-hexahydro-2H-pyrido[1',2':4,5]pyrazino[2,1-b][1,3]oxazine-9-carboxamide(Non-covalent)

DLU.3: 11 residues within 4Å: Chain A: D.65, D.117, P.146, Q.147, E.153 Chain J: G.5 Chain K: C.29, A.30 Ligands: CL.2, MG.4, MG.5 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.146 Hydrogen bonds: A:D.117, A:D.117 Water bridges: A:C.66 Salt bridges: A:D.117 DLU.11: 11 residues within 4Å: Chain B: G.5 Chain C: C.29, A.30 Chain I: D.65, D.117, P.146, Q.147, E.153 Ligands: CL.10, MG.12, MG.13 4 PLIP interactions: 4 interactions with chain I Hydrophobic interactions: I:P.146 Hydrogen bonds: I:D.117, I:D.117 Water bridges: I:C.66

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: D.65, D.117 Ligands: DLU.3, MG.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.65, A:D.117, H2O.1, H2O.1 MG.5: 4 residues within 4Å: Chain A: D.65, E.153 Ligands: DLU.3, MG.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.65, A:E.153, A:E.153, H2O.1 MG.12: 4 residues within 4Å: Chain I: D.65, D.117 Ligands: DLU.11, MG.13 4 PLIP interactions: 2 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:D.65, I:D.117, H2O.1, H2O.1 MG.13: 4 residues within 4Å: Chain I: D.65, E.153 Ligands: DLU.11, MG.12 4 PLIP interactions: 3 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:D.65, I:E.153, I:E.153, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cook, N.J. et al., Structural basis of second-generation HIV integrase inhibitor action and viral resistance. Science (2020)

Release Date

2020-02-05

Peptides

Pol protein: ADEFGHILMNOP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
E

E
N

F
L

G
K

H
J

I
I

L
M

M
F

N
D

O
C

P
B

Pol protein

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