SMTL ID : 9dwd.1

Gag CA-SP1 immature lattice bound with Lenacapavir from enveloped virus like particles (T8I)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-18-mer

Ligands

18 x QNG: N-[(1S)-1-(3-{4-chloro-3-[(methylsulfonyl)amino]-1-(2,2,2-trifluoroethyl)-1H-indazol-7-yl}-6-[3-methyl-3-(methylsulfonyl)but-1-yn-1-yl]pyridin-2-yl)-2-(3,5-difluorophenyl)ethyl]-2-[(3bS,4aR)-5,5-difluoro-3-(trifluoromethyl)-3b,4,4a,5-tetrahydro-1H-cyclopropa[3,4]cyclopenta[1,2-c]pyrazol-1-yl]acetamide(Non-covalent)

QNG.1: 21 residues within 4Å: Chain A: Q.42, N.45, T.46, L.48, N.49, Q.55, M.58, Q.59, L.61, K.62, I.65, N.66, A.97, T.99, Y.122 Chain B: I.7, S.8, P.9, R.10, N.13 Chain D: R.74 17 PLIP interactions: 2 interactions with chain B, 15 interactions with chain A Hydrophobic interactions: B:P.9, A:Q.42, A:N.45, A:L.48, A:L.48, A:A.97, A:T.99 pi-Cation interactions: B:R.10, A:K.62, A:K.62 Hydrogen bonds: A:N.49, A:N.49, A:K.62, A:N.66, A:N.66 Halogen bonds: A:N.49, A:Q.55 QNG.2: 21 residues within 4Å: Chain A: I.7, S.8, P.9, R.10, N.13 Chain B: Q.42, N.45, T.46, L.48, N.49, Q.55, M.58, Q.59, L.61, K.62, I.65, N.66, A.97, T.99, Y.122 Chain C: R.74 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Q.42, B:N.45, B:L.48, B:K.62, B:A.97, B:T.99, A:P.9 Hydrogen bonds: B:N.49, B:N.49, B:K.62, B:N.66, B:N.66 Halogen bonds: B:N.49, B:Q.55 pi-Cation interactions: A:R.10 QNG.3: 15 residues within 4Å: Chain C: Q.42, N.45, T.46, L.48, N.49, Q.55, M.58, Q.59, L.61, K.62, I.65, N.66, A.97, T.99, Y.122 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:Q.42, C:N.45, C:L.48, C:L.48, C:M.58, C:L.61 Hydrogen bonds: C:N.49, C:K.62, C:N.66, C:N.66, C:T.99 pi-Cation interactions: C:K.62 Halogen bonds: C:Q.55 QNG.4: 22 residues within 4Å: Chain D: Q.42, N.45, T.46, L.48, N.49, Q.55, M.58, Q.59, L.61, K.62, I.65, N.66, A.97, G.98, T.99, Y.122 Chain E: I.7, P.9, R.10, L.12, N.13 Chain G: R.74 16 PLIP interactions: 2 interactions with chain E, 14 interactions with chain D Hydrophobic interactions: E:P.9, D:Q.42, D:N.45, D:L.48, D:L.48, D:M.58, D:K.62, D:A.97, D:T.99 pi-Cation interactions: E:R.10 Hydrogen bonds: D:N.49, D:N.49, D:K.62, D:N.66, D:N.66 Halogen bonds: D:N.49 QNG.5: 20 residues within 4Å: Chain D: I.7, S.8, P.9, R.10, N.13 Chain E: N.45, T.46, L.48, N.49, Q.55, M.58, Q.59, L.61, K.62, I.65, N.66, A.97, T.99, Y.122 Chain F: R.74 15 PLIP interactions: 13 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:N.45, E:L.48, E:L.48, E:M.58, E:A.97, E:T.99, D:P.9 Hydrogen bonds: E:N.49, E:N.49, E:K.62, E:N.66 pi-Cation interactions: E:K.62, D:R.10 Halogen bonds: E:N.49, E:Q.55 QNG.6: 15 residues within 4Å: Chain F: Q.42, N.45, T.46, L.48, N.49, Q.55, M.58, Q.59, L.61, K.62, I.65, N.66, A.97, T.99, Y.122 14 PLIP interactions: 14 interactions with chain F Hydrophobic interactions: F:Q.42, F:N.45, F:L.48, F:L.48, F:I.65, F:T.99 Hydrogen bonds: F:N.49, F:N.49, F:K.62, F:N.66, F:N.66 pi-Cation interactions: F:K.62, F:K.62 Halogen bonds: F:Q.55 QNG.8: 22 residues within 4Å: Chain G: Q.42, N.45, T.46, L.48, N.49, Q.55, M.58, Q.59, L.61, K.62, I.65, N.66, A.97, G.98, T.99, Y.122 Chain H: I.7, S.8, P.9, R.10, N.13 Chain J: R.74 17 PLIP interactions: 14 interactions with chain G, 3 interactions with chain H Hydrophobic interactions: G:Q.42, G:N.45, G:L.48, G:L.48, G:M.58, G:A.97, H:P.9, H:N.13 Hydrogen bonds: G:N.49, G:N.49, G:K.62, G:N.66, G:N.66, G:T.99 pi-Cation interactions: G:K.62, H:R.10 Halogen bonds: G:N.49 QNG.9: 22 residues within 4Å: Chain G: I.7, S.8, P.9, R.10, L.12, N.13 Chain H: Q.42, N.45, T.46, L.48, N.49, Q.55, M.58, Q.59, L.61, K.62, I.65, N.66, A.97, T.99, Y.122 Chain I: R.74 17 PLIP interactions: 15 interactions with chain H, 2 interactions with chain G Hydrophobic interactions: H:Q.42, H:N.45, H:L.48, H:L.48, H:A.97, H:T.99, G:P.9 Hydrogen bonds: H:N.49, H:N.49, H:K.62, H:N.66, H:N.66 pi-Cation interactions: H:K.62, G:R.10 Halogen bonds: H:N.49, H:N.49, H:Q.55 QNG.10: 15 residues within 4Å: Chain I: Q.42, N.45, T.46, L.48, N.49, Q.55, M.58, Q.59, L.61, K.62, I.65, N.66, A.97, T.99, Y.122 11 PLIP interactions: 11 interactions with chain I Hydrophobic interactions: I:Q.42, I:N.45, I:L.48, I:L.48, I:A.97 Hydrogen bonds: I:N.49, I:K.62, I:N.66, I:N.66, I:T.99 pi-Cation interactions: I:K.62 QNG.11: 21 residues within 4Å: Chain J: Q.42, N.45, T.46, L.48, N.49, Q.55, M.58, Q.59, L.61, K.62, I.65, N.66, A.97, T.99, Y.122 Chain K: I.7, S.8, P.9, R.10, N.13 Chain M: R.74 17 PLIP interactions: 2 interactions with chain K, 15 interactions with chain J Hydrophobic interactions: K:P.9, J:Q.42, J:N.45, J:L.48, J:M.58, J:K.62, J:A.97, J:T.99 pi-Cation interactions: K:R.10, J:K.62, J:K.62 Hydrogen bonds: J:N.49, J:N.49, J:K.62, J:N.66, J:N.66 Halogen bonds: J:N.49 QNG.12: 22 residues within 4Å: Chain J: I.7, S.8, P.9, R.10, L.12, N.13 Chain K: Q.42, N.45, T.46, L.48, N.49, Q.55, M.58, Q.59, L.61, K.62, I.65, N.66, A.97, T.99, Y.122 Chain L: R.74 16 PLIP interactions: 14 interactions with chain K, 2 interactions with chain J Hydrophobic interactions: K:Q.42, K:N.45, K:L.48, K:L.48, K:M.58, K:A.97, K:T.99, J:P.9 Hydrogen bonds: K:N.49, K:N.49, K:K.62, K:N.66, K:N.66 Halogen bonds: K:N.49, K:Q.55 pi-Cation interactions: J:R.10 QNG.13: 16 residues within 4Å: Chain L: Q.42, N.45, T.46, L.48, N.49, Q.55, M.58, Q.59, L.61, K.62, I.65, N.66, A.97, G.98, T.99, Y.122 13 PLIP interactions: 13 interactions with chain L Hydrophobic interactions: L:Q.42, L:N.45, L:L.48, L:L.48, L:M.58, L:I.65 Hydrogen bonds: L:N.49, L:K.62, L:N.66, L:N.66 pi-Cation interactions: L:K.62 Halogen bonds: L:Q.55, L:Q.59 QNG.14: 21 residues within 4Å: Chain M: Q.42, N.45, T.46, L.48, N.49, Q.55, M.58, Q.59, L.61, K.62, I.65, N.66, A.97, T.99, Y.122 Chain N: I.7, S.8, P.9, R.10, N.13 Chain P: R.74 17 PLIP interactions: 15 interactions with chain M, 2 interactions with chain N Hydrophobic interactions: M:Q.42, M:N.45, M:L.48, M:L.48, M:Q.55, M:M.58, M:K.62, M:A.97, M:T.99, N:P.9 Hydrogen bonds: M:N.49, M:N.49, M:K.62, M:N.66, M:N.66 Halogen bonds: M:N.49 pi-Cation interactions: N:R.10 QNG.15: 21 residues within 4Å: Chain M: I.7, S.8, P.9, R.10, N.13 Chain N: Q.42, N.45, T.46, L.48, N.49, Q.55, M.58, Q.59, L.61, K.62, I.65, N.66, A.97, T.99, Y.122 Chain O: R.74 16 PLIP interactions: 14 interactions with chain N, 2 interactions with chain M Hydrophobic interactions: N:Q.42, N:N.45, N:L.48, N:L.48, N:M.58, N:A.97, N:T.99, M:P.9 Hydrogen bonds: N:N.49, N:K.62, N:N.66, N:N.66 pi-Cation interactions: N:K.62, M:R.10 Halogen bonds: N:N.49, N:Q.55 QNG.16: 15 residues within 4Å: Chain O: Q.42, N.45, T.46, L.48, N.49, Q.55, M.58, Q.59, L.61, K.62, I.65, N.66, A.97, T.99, Y.122 11 PLIP interactions: 11 interactions with chain O Hydrophobic interactions: O:Q.42, O:N.45, O:L.48, O:L.48, O:I.65, O:T.99 Hydrogen bonds: O:N.49, O:K.62, O:N.66, O:N.66 pi-Cation interactions: O:K.62 QNG.17: 20 residues within 4Å: Chain A: R.74 Chain P: Q.42, N.45, T.46, L.48, N.49, Q.55, M.58, Q.59, L.61, K.62, I.65, N.66, A.97, T.99, Y.122 Chain Q: I.7, P.9, R.10, N.13 19 PLIP interactions: 3 interactions with chain Q, 16 interactions with chain P Hydrophobic interactions: Q:P.9, Q:N.13, P:Q.42, P:N.45, P:L.48, P:L.48, P:M.58, P:A.97, P:T.99 pi-Cation interactions: Q:R.10, P:K.62, P:K.62 Hydrogen bonds: P:N.49, P:N.49, P:K.62, P:N.66, P:N.66 Halogen bonds: P:N.49, P:Q.55 QNG.18: 21 residues within 4Å: Chain P: I.7, S.8, P.9, R.10, N.13 Chain Q: Q.42, N.45, T.46, L.48, N.49, Q.55, M.58, Q.59, L.61, K.62, I.65, N.66, A.97, T.99, Y.122 Chain R: R.74 19 PLIP interactions: 3 interactions with chain P, 16 interactions with chain Q Hydrophobic interactions: P:P.9, Q:Q.42, Q:N.45, Q:L.48, Q:L.48, Q:M.58, Q:A.97, Q:T.99 Hydrogen bonds: P:R.10, Q:N.49, Q:N.49, Q:K.62, Q:N.66, Q:N.66 pi-Cation interactions: P:R.10, Q:K.62 Halogen bonds: Q:N.49, Q:N.49, Q:Q.55 QNG.19: 15 residues within 4Å: Chain R: Q.42, N.45, T.46, L.48, N.49, Q.55, M.58, Q.59, L.61, K.62, I.65, N.66, A.97, T.99, Y.122 9 PLIP interactions: 9 interactions with chain R Hydrophobic interactions: R:Q.42, R:N.45, R:L.48, R:L.48 Hydrogen bonds: R:N.49, R:K.62, R:N.66, R:N.66 pi-Cation interactions: R:K.62

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.7: 11 residues within 4Å: Chain A: K.150, K.219 Chain D: K.150, K.219 Chain G: K.150, K.219 Chain J: K.150, K.219 Chain M: K.150, K.219 Chain P: K.150 19 PLIP interactions: 2 interactions with chain P, 3 interactions with chain M, 3 interactions with chain J, 4 interactions with chain D, 4 interactions with chain G, 3 interactions with chain A Salt bridges: P:K.150, P:K.150, M:K.150, M:K.150, M:K.219, J:K.150, J:K.150, J:K.219, D:K.150, D:K.150, D:K.219, D:K.219, G:K.150, G:K.150, G:K.219, G:K.219, A:K.150, A:K.219, A:K.219

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, C. et al., Structural insights into inhibitor mechanisms on immature HIV-1 Gag lattice revealed by high-resolution in situ single-particle cryo-EM. Biorxiv (2024)

Release Date

2024-10-30

Peptides

Gag: ABCDEFGHIJKLMNOPQR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
Q

R
R

Gag

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