SMTL ID : 6rwm.1

SIVrcm intasome in complex with bictegravir

Coordinates

PDB Format

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 B: H.13, H.17, C.41, C.44 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.13, B:H.17, B:C.41, B:C.44 ZN.7: 4 residues within 4Å: Chain C: H.13, H.17, C.41, C.44 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.13, C:H.17, C:C.41, C:C.44 ZN.8: 4 residues within 4Å: Chain F: H.13, H.17, C.41, C.44 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.13, F:H.17, F:C.41, F: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 J: H.13, H.17, C.41, C.44 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:H.13, J:H.17, J:C.41, J:C.44 ZN.15: 4 residues within 4Å: Chain K: H.13, H.17, C.41, C.44 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:H.13, K:H.17, K:C.41, K:C.44 ZN.16: 4 residues within 4Å: Chain N: H.13, H.17, C.41, C.44 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:H.13, N:H.17, N:C.41, N:C.44

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.65, D.117 Ligands: MG.3, KLQ.4 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.3: 4 residues within 4Å: Chain A: D.65, E.153 Ligands: MG.2, KLQ.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.2 MG.10: 4 residues within 4Å: Chain I: D.65, D.117 Ligands: MG.11, KLQ.12 4 PLIP interactions: 2 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:D.65, I:D.117, H2O.3, H2O.3 MG.11: 4 residues within 4Å: Chain I: D.65, E.153 Ligands: MG.10, KLQ.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.3

2 x KLQ: Bictegravir(Non-covalent)

KLQ.4: 14 residues within 4Å: Chain A: D.65, D.117, N.118, G.119, Y.144, P.146, Q.147, E.153 Chain G: C.29, A.30 Chain H: G.5 Ligands: MG.2, MG.3, CL.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, A:E.153 KLQ.12: 14 residues within 4Å: Chain I: D.65, D.117, N.118, G.119, Y.144, P.146, Q.147, E.153 Chain O: C.29, A.30 Chain P: G.5 Ligands: MG.10, MG.11, CL.13 5 PLIP interactions: 5 interactions with chain I Hydrophobic interactions: I:P.146 Hydrogen bonds: I:D.117, I:D.117 Water bridges: I:C.66, I:E.153

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

CL.5: 4 residues within 4Å: Chain A: N.118, P.143, Y.144 Ligands: KLQ.4 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain I: N.118, P.143, Y.144 Ligands: KLQ.12 Ligand excluded by PLIP

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: ABCDEFIJKLMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
F

F
M

I
I

J
J

K
K

L
L

M
N

N
E

Pol protein

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