SMTL ID : 9d6c.1

Gag CA-SP1 immature lattice bound with Lenacapavir and Bevirimat from enveloped virus like particles

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-18-mer

Ligands

18 x QNG: Lenacapavir(Non-covalent)

QNG.1: 23 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, G.98, T.99, Y.122 Chain B: I.7, S.8, P.9, R.10, N.13 Chain D: E.71, R.74 17 PLIP interactions: 14 interactions with chain A, 1 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: A:Q.42, A:L.48, A:L.48, A:A.97, A:T.99, B:P.9 Hydrogen bonds: A:N.49, A:N.49, A:K.62, A:N.66, A:N.66 pi-Cation interactions: A:K.62, A:K.62, B:R.10 Halogen bonds: A:N.49, A:Q.55, D:E.71 QNG.2: 23 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, G.98, T.99, Y.122 Chain C: E.71, R.74 17 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 14 interactions with chain B Hydrophobic interactions: A:P.9, B:Q.42, B:L.48, B:L.48, B:T.99 pi-Cation interactions: A:R.10, B:K.62, B:K.62 Halogen bonds: C:E.71, B:N.49, B:N.49, B:Q.55 Hydrogen bonds: B:N.49, B:N.49, B:K.62, B:N.66, B:N.66 QNG.5: 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 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:Q.42, C:N.45, C:L.48, C:L.48, C:A.97, C:T.99 Hydrogen bonds: C:N.49, C:N.49, C:K.62, C:N.66, C:N.66 pi-Cation interactions: C:K.62, C:K.62 Halogen bonds: C:N.49, C:Q.55 QNG.7: 23 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, S.8, P.9, R.10, N.13 Chain G: E.71, R.74 16 PLIP interactions: 14 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:Q.42, D:L.48, D:L.48, D:A.97, D:T.99, E:P.9 Hydrogen bonds: D:N.49, D:N.49, D:K.62, D:N.66, D:N.66 pi-Cation interactions: D:K.62, D:K.62, E:R.10 Halogen bonds: D:N.49, D:Q.55 QNG.8: 23 residues within 4Å: Chain D: I.7, S.8, P.9, R.10, N.13 Chain E: 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 F: E.71, R.74 16 PLIP interactions: 14 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:Q.42, E:L.48, E:L.48, E:T.99, D:P.9 Hydrogen bonds: E:N.49, E:N.49, E:K.62, E:N.66, E:N.66 pi-Cation interactions: E:K.62, E:K.62, D:R.10 Halogen bonds: E:N.49, E:N.49, E:Q.55 QNG.11: 16 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, G.98, T.99, Y.122 14 PLIP interactions: 14 interactions with chain F Hydrophobic interactions: F:Q.42, F:L.48, F:L.48, F:A.97, 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:N.49, F:Q.55 QNG.12: 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, T.99, Y.122 Chain H: I.7, S.8, P.9, R.10, N.13 Chain J: E.71, R.74 17 PLIP interactions: 2 interactions with chain H, 14 interactions with chain G, 1 interactions with chain J Hydrophobic interactions: H:P.9, G:Q.42, G:L.48, G:L.48, G:A.97, G:T.99 pi-Cation interactions: H:R.10, G:K.62, G:K.62 Hydrogen bonds: G:N.49, G:N.49, G:K.62, G:N.66, G:N.66 Halogen bonds: G:N.49, G:Q.55, J:E.71 QNG.13: 23 residues within 4Å: Chain G: I.7, S.8, P.9, R.10, 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, G.98, T.99, Y.122 Chain I: E.71, R.74 17 PLIP interactions: 15 interactions with chain H, 2 interactions with chain G Hydrophobic interactions: H:Q.42, H:L.48, H:L.48, H:M.58, 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, H:K.62, G:R.10 Halogen bonds: H:N.49, H:N.49, H:Q.55 QNG.16: 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 15 PLIP interactions: 15 interactions with chain I Hydrophobic interactions: I:Q.42, I:N.45, I:L.48, I:L.48, I:M.58, I:T.99 Hydrogen bonds: I:N.49, I:N.49, I:K.62, I:N.66, I:N.66 pi-Cation interactions: I:K.62, I:K.62 Halogen bonds: I:N.49, I:Q.55 QNG.17: 22 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: E.71, R.74 16 PLIP interactions: 14 interactions with chain J, 2 interactions with chain K Hydrophobic interactions: J:Q.42, J:L.48, J:L.48, J:A.97, J:T.99, K:P.9 Hydrogen bonds: J:N.49, J:N.49, J:K.62, J:N.66, J:N.66 pi-Cation interactions: J:K.62, J:K.62, K:R.10 Halogen bonds: J:N.49, J:Q.55 QNG.18: 23 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: E.71, R.74 17 PLIP interactions: 14 interactions with chain K, 2 interactions with chain J, 1 interactions with chain L Hydrophobic interactions: K:Q.42, K:L.48, K:L.48, K:T.99, J:P.9 Hydrogen bonds: K:N.49, K:N.49, K:K.62, K:N.66, K:N.66 pi-Cation interactions: K:K.62, K:K.62, J:R.10 Halogen bonds: K:N.49, K:N.49, K:Q.55, L:E.71 QNG.21: 15 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, T.99, Y.122 15 PLIP interactions: 15 interactions with chain L Hydrophobic interactions: L:Q.42, L:N.45, L:L.48, L:L.48, L:A.97, L:T.99 Hydrogen bonds: L:N.49, L:N.49, L:K.62, L:N.66, L:N.66 pi-Cation interactions: L:K.62, L:K.62 Halogen bonds: L:N.49, L:Q.55 QNG.23: 22 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: E.71, R.74 16 PLIP interactions: 14 interactions with chain M, 2 interactions with chain N Hydrophobic interactions: M:Q.42, M:L.48, M:L.48, 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 pi-Cation interactions: M:K.62, M:K.62, N:R.10 Halogen bonds: M:N.49, M:Q.55 QNG.24: 23 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, G.98, T.99, Y.122 Chain O: E.71, R.74 17 PLIP interactions: 15 interactions with chain N, 2 interactions with chain M Hydrophobic interactions: N:Q.42, N:L.48, N:L.48, N:M.58, N:T.99, M:P.9 Hydrogen bonds: N:N.49, N:N.49, N:K.62, N:N.66, N:N.66 pi-Cation interactions: N:K.62, N:K.62, M:R.10 Halogen bonds: N:N.49, N:N.49, N:Q.55 QNG.27: 16 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, G.98, T.99, Y.122 14 PLIP interactions: 14 interactions with chain O Hydrophobic interactions: O:Q.42, O:L.48, O:L.48, O:A.97, O:T.99 Hydrogen bonds: O:N.49, O:N.49, O:K.62, O:N.66, O:N.66 pi-Cation interactions: O:K.62, O:K.62 Halogen bonds: O:N.49, O:Q.55 QNG.28: 22 residues within 4Å: Chain A: E.71, 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, S.8, P.9, R.10, N.13 18 PLIP interactions: 15 interactions with chain P, 1 interactions with chain A, 2 interactions with chain Q Hydrophobic interactions: P:Q.42, P:N.45, P:L.48, P:L.48, P:A.97, P:T.99, Q:P.9 Hydrogen bonds: P:N.49, P:N.49, P:K.62, P:N.66, P:N.66 pi-Cation interactions: P:K.62, P:K.62, Q:R.10 Halogen bonds: P:N.49, P:Q.55, A:E.71 QNG.29: 23 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, G.98, T.99, Y.122 Chain R: E.71, R.74 17 PLIP interactions: 14 interactions with chain Q, 1 interactions with chain R, 2 interactions with chain P Hydrophobic interactions: Q:Q.42, Q:L.48, Q:L.48, Q:M.58, Q:T.99, P:P.9 Hydrogen bonds: Q:N.49, Q:N.49, Q:K.62, Q:N.66, Q:N.66 pi-Cation interactions: Q:K.62, Q:K.62, P:R.10 Halogen bonds: Q:N.49, Q:Q.55, R:E.71 QNG.32: 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 14 PLIP interactions: 14 interactions with chain R Hydrophobic interactions: R:Q.42, R:N.45, R:L.48, R:L.48, R:T.99 Hydrogen bonds: R:N.49, R:N.49, R:K.62, R:N.66, R:N.66 pi-Cation interactions: R:K.62, R:K.62 Halogen bonds: R:N.49, R:Q.55

7 x 2I4: 3alpha-[(3-carboxy-3-methylbutanoyl)oxy]-8alpha,9beta,10alpha,13alpha,17alpha,19beta-lup-20(29)-en-28-oic acid(Non-covalent)

2I4.3: 5 residues within 4Å: Chain B: L.223, M.227, I.231 Chain C: L.223, M.227 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.223 2I4.6: 14 residues within 4Å: Chain A: L.223, M.227 Chain D: K.219, L.223, M.227, I.231 Chain G: L.223, I.231 Chain J: L.223, M.227 Chain M: L.223, M.227 Chain P: L.223, M.227 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain J, 1 interactions with chain P Hydrophobic interactions: D:M.227, D:I.231, J:L.223, P:L.223 Salt bridges: D:K.219 2I4.9: 5 residues within 4Å: Chain E: L.223, M.227, I.231 Chain F: L.223, M.227 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:L.223 2I4.14: 5 residues within 4Å: Chain H: L.223, M.227, I.231 Chain I: L.223, M.227 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:L.223 2I4.19: 5 residues within 4Å: Chain K: L.223, M.227, I.231 Chain L: L.223, M.227 1 PLIP interactions: 1 interactions with chain L Hydrophobic interactions: L:L.223 2I4.25: 4 residues within 4Å: Chain N: L.223, M.227, I.231 Chain O: L.223 1 PLIP interactions: 1 interactions with chain O Hydrophobic interactions: O:L.223 2I4.30: 5 residues within 4Å: Chain Q: L.223, M.227, I.231 Chain R: L.223, M.227 1 PLIP interactions: 1 interactions with chain R Hydrophobic interactions: R:L.223

7 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.4: 4 residues within 4Å: Chain B: K.150, K.219 Chain C: K.150, K.219 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain B Salt bridges: C:K.150, C:K.219, C:K.219, B:K.150, B:K.150, B:K.219, B:K.219 IHP.10: 4 residues within 4Å: Chain E: K.150, K.219 Chain F: K.150, K.219 7 PLIP interactions: 3 interactions with chain F, 4 interactions with chain E Salt bridges: F:K.150, F:K.219, F:K.219, E:K.150, E:K.150, E:K.219, E:K.219 IHP.15: 4 residues within 4Å: Chain H: K.150, K.219 Chain I: K.150, K.219 7 PLIP interactions: 3 interactions with chain I, 4 interactions with chain H Salt bridges: I:K.150, I:K.219, I:K.219, H:K.150, H:K.150, H:K.219, H:K.219 IHP.20: 4 residues within 4Å: Chain K: K.150, K.219 Chain L: K.150, K.219 7 PLIP interactions: 4 interactions with chain K, 3 interactions with chain L Salt bridges: K:K.150, K:K.150, K:K.219, K:K.219, L:K.150, L:K.219, L:K.219 IHP.22: 12 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, K.219 13 PLIP interactions: 1 interactions with chain D, 2 interactions with chain J, 3 interactions with chain G, 3 interactions with chain M, 1 interactions with chain P, 3 interactions with chain A Salt bridges: D:K.150, J:K.150, J:K.219, G:K.150, G:K.219, G:K.219, M:K.150, M:K.150, M:K.219, P:K.150, A:K.150, A:K.219, A:K.219 IHP.26: 4 residues within 4Å: Chain N: K.150, K.219 Chain O: K.150, K.219 7 PLIP interactions: 4 interactions with chain N, 3 interactions with chain O Salt bridges: N:K.150, N:K.150, N:K.219, N:K.219, O:K.150, O:K.219, O:K.219 IHP.31: 4 residues within 4Å: Chain Q: K.150, K.219 Chain R: K.150, K.219 6 PLIP interactions: 3 interactions with chain Q, 3 interactions with chain R Salt bridges: Q:K.150, Q:K.219, Q:K.219, R:K.150, R:K.219, R: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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