SMTL ID : 7rhn.1

Co-crystal structure of Q67H mutant of disulfide stabilized HIV-1 CA hexamer and lenacapavir

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.46 Å

Oligo State

homo-hexamer

Ligands

6 x QNG: Lenacapavir(Non-covalent)

QNG.1: 21 residues within 4Å: Chain A: N.53, L.56, N.57, Q.63, M.66, L.69, K.70, I.73, N.74, A.105, G.106, T.107, Y.130 Chain F: I.37, P.38, S.41, I.135, Y.169, L.172, R.173 Ligands: CL.5 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain F Hydrophobic interactions: A:L.56, A:L.56, A:K.70, A:K.70, A:T.107, F:P.38 Hydrogen bonds: A:N.57, A:N.57, A:K.70, A:N.74, A:N.74 pi-Cation interactions: A:K.70, A:K.70, A:K.70 Halogen bonds: A:K.70, A:N.74, F:Y.169 QNG.9: 21 residues within 4Å: Chain B: N.53, L.56, N.57, Q.63, M.66, L.69, K.70, I.73, N.74, A.105, G.106, T.107, Y.130 Chain D: I.37, P.38, S.41, I.135, Y.169, L.172, R.173 Ligands: CL.13 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:L.56, B:L.56, B:K.70, B:K.70, B:T.107, D:P.38 Hydrogen bonds: B:N.57, B:N.57, B:K.70, B:N.74, B:N.74 pi-Cation interactions: B:K.70, B:K.70, B:K.70 Halogen bonds: B:K.70, B:N.74, D:Y.169 QNG.17: 21 residues within 4Å: Chain C: N.53, L.56, N.57, Q.63, M.66, L.69, K.70, I.73, N.74, A.105, G.106, T.107, Y.130 Chain E: I.37, P.38, S.41, I.135, Y.169, L.172, R.173 Ligands: CL.21 17 PLIP interactions: 2 interactions with chain E, 15 interactions with chain C Hydrophobic interactions: E:P.38, C:L.56, C:L.56, C:K.70, C:K.70, C:T.107 Halogen bonds: E:Y.169, C:K.70, C:N.74 Hydrogen bonds: C:N.57, C:N.57, C:K.70, C:N.74, C:N.74 pi-Cation interactions: C:K.70, C:K.70, C:K.70 QNG.25: 21 residues within 4Å: Chain C: I.37, P.38, S.41, I.135, Y.169, L.172, R.173 Chain D: N.53, L.56, N.57, Q.63, M.66, L.69, K.70, I.73, N.74, A.105, G.106, T.107, Y.130 Ligands: CL.29 17 PLIP interactions: 15 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:L.56, D:L.56, D:K.70, D:K.70, D:T.107, C:P.38 Hydrogen bonds: D:N.57, D:N.57, D:K.70, D:N.74, D:N.74 pi-Cation interactions: D:K.70, D:K.70, D:K.70 Halogen bonds: D:K.70, D:N.74, C:Y.169 QNG.33: 21 residues within 4Å: Chain A: I.37, P.38, S.41, I.135, Y.169, L.172, R.173 Chain E: N.53, L.56, N.57, Q.63, M.66, L.69, K.70, I.73, N.74, A.105, G.106, T.107, Y.130 Ligands: CL.37 17 PLIP interactions: 2 interactions with chain A, 15 interactions with chain E Hydrophobic interactions: A:P.38, E:L.56, E:L.56, E:K.70, E:K.70, E:T.107 Halogen bonds: A:Y.169, E:K.70, E:N.74 Hydrogen bonds: E:N.57, E:N.57, E:K.70, E:N.74, E:N.74 pi-Cation interactions: E:K.70, E:K.70, E:K.70 QNG.41: 21 residues within 4Å: Chain B: I.37, P.38, S.41, I.135, Y.169, L.172, R.173 Chain F: N.53, L.56, N.57, Q.63, M.66, L.69, K.70, I.73, N.74, A.105, G.106, T.107, Y.130 Ligands: CL.45 17 PLIP interactions: 15 interactions with chain F, 2 interactions with chain B Hydrophobic interactions: F:L.56, F:L.56, F:K.70, F:K.70, F:T.107, B:P.38 Hydrogen bonds: F:N.57, F:N.57, F:K.70, F:N.74, F:N.74 pi-Cation interactions: F:K.70, F:K.70, F:K.70 Halogen bonds: F:K.70, F:N.74, B:Y.169

18 x IOD: IODIDE ION(Non-functional Binders)

IOD.2: 2 residues within 4Å: Chain A: P.17, R.18 Ligand excluded by PLIP IOD.3: 5 residues within 4Å: Chain A: E.35, R.173 Chain E: G.60, G.61, Q.63 Ligand excluded by PLIP IOD.4: 2 residues within 4Å: Chain A: P.17, N.21 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain B: P.17, R.18 Ligand excluded by PLIP IOD.11: 5 residues within 4Å: Chain B: E.35, R.173 Chain F: G.60, G.61, Q.63 Ligand excluded by PLIP IOD.12: 2 residues within 4Å: Chain B: P.17, N.21 Ligand excluded by PLIP IOD.18: 2 residues within 4Å: Chain C: P.17, R.18 Ligand excluded by PLIP IOD.19: 5 residues within 4Å: Chain C: E.35, R.173 Chain D: G.60, G.61, Q.63 Ligand excluded by PLIP IOD.20: 2 residues within 4Å: Chain C: P.17, N.21 Ligand excluded by PLIP IOD.26: 2 residues within 4Å: Chain D: P.17, R.18 Ligand excluded by PLIP IOD.27: 5 residues within 4Å: Chain B: G.60, G.61, Q.63 Chain D: E.35, R.173 Ligand excluded by PLIP IOD.28: 2 residues within 4Å: Chain D: P.17, N.21 Ligand excluded by PLIP IOD.34: 2 residues within 4Å: Chain E: P.17, R.18 Ligand excluded by PLIP IOD.35: 5 residues within 4Å: Chain C: G.60, G.61, Q.63 Chain E: E.35, R.173 Ligand excluded by PLIP IOD.36: 2 residues within 4Å: Chain E: P.17, N.21 Ligand excluded by PLIP IOD.42: 2 residues within 4Å: Chain F: P.17, R.18 Ligand excluded by PLIP IOD.43: 5 residues within 4Å: Chain A: G.60, G.61, Q.63 Chain F: E.35, R.173 Ligand excluded by PLIP IOD.44: 2 residues within 4Å: Chain F: P.17, N.21 Ligand excluded by PLIP

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

CL.5: 3 residues within 4Å: Chain A: N.57 Chain F: R.173 Ligands: QNG.1 Ligand excluded by PLIP CL.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: R.162, Q.219 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: V.27, E.28, G.60, H.62 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: N.57 Chain D: R.173 Ligands: QNG.9 Ligand excluded by PLIP CL.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain B: R.162, Q.219 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain B: V.27, E.28, G.60, H.62 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain C: N.57 Chain E: R.173 Ligands: QNG.17 Ligand excluded by PLIP CL.22: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain C: R.162, Q.219 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain C: V.27, E.28, G.60, H.62 Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain C: R.173 Chain D: N.57 Ligands: QNG.25 Ligand excluded by PLIP CL.30: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.31: 2 residues within 4Å: Chain D: R.162, Q.219 Ligand excluded by PLIP CL.32: 4 residues within 4Å: Chain D: V.27, E.28, G.60, H.62 Ligand excluded by PLIP CL.37: 3 residues within 4Å: Chain A: R.173 Chain E: N.57 Ligands: QNG.33 Ligand excluded by PLIP CL.38: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.39: 2 residues within 4Å: Chain E: R.162, Q.219 Ligand excluded by PLIP CL.40: 4 residues within 4Å: Chain E: V.27, E.28, G.60, H.62 Ligand excluded by PLIP CL.45: 3 residues within 4Å: Chain B: R.173 Chain F: N.57 Ligands: QNG.41 Ligand excluded by PLIP CL.46: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.47: 2 residues within 4Å: Chain F: R.162, Q.219 Ligand excluded by PLIP CL.48: 4 residues within 4Å: Chain F: V.27, E.28, G.60, H.62 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bester, S.M. et al., Structural and Mechanistic Bases of Viral Resistance to HIV-1 Capsid Inhibitor Lenacapavir. Mbio (2022)

Release Date

2022-07-27

Peptides

Capsid protein p24: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
C

C
C

D
C

E
C

F
C

Capsid protein p24

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